Starting phenix.real_space_refine on Thu Mar 5 23:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vrv_32107/03_2026/7vrv_32107.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 114 5.16 5 C 16623 2.51 5 N 4277 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26151 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.01, per 1000 atoms: 0.23 Number of scatterers: 26151 At special positions: 0 Unit cell: (154.96, 160.16, 193.44, 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 114 16.00 O 5137 8.00 N 4277 7.00 C 16623 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.04 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 702 " " NAG A1310 " - " ASN A1067 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 702 " " NAG B1309 " - " ASN B 710 " " NAG B1310 " - " ASN B1067 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 702 " " NAG C1310 " - " ASN C1067 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 710 " " NAG F 1 " - " ASN A 794 " " NAG G 1 " - " ASN A1091 " " NAG H 1 " - " ASN A1127 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B 794 " " NAG K 1 " - " ASN B1091 " " NAG L 1 " - " ASN B1127 " " NAG M 1 " - " ASN C 710 " " NAG N 1 " - " ASN C 794 " " NAG O 1 " - " ASN C1091 " " NAG P 1 " - " ASN C1127 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 23.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.722A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.898A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.387A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.298A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 751 through 776 removed outlier: 3.869A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 3.896A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.673A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 911 removed outlier: 3.973A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.657A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.102A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.828A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.673A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.839A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.641A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.786A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.733A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.716A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.535A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.715A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 848 " --> pdb=" O CYS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 848' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 883 removed outlier: 3.900A pdb=" N GLY B 882 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.712A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.020A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.859A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 3.987A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.689A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 818 removed outlier: 4.124A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.091A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.347A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.100A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.534A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.701A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1139 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.521A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.642A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.666A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.406A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.823A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.930A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AB9, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.590A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.812A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.510A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.640A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.205A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.665A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 704 through 713 removed outlier: 6.360A pdb=" N GLN B1064 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE B 711 " --> pdb=" O PRO B1062 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 713 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B1060 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 720 removed outlier: 4.174A pdb=" N THR B1069 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B1088 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.004A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 5.146A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.571A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.507A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.549A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.896A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.419A pdb=" N THR C 689 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AE7, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AE8, first strand: chain 'C' and resid 1087 through 1089 913 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8334 1.34 - 1.47: 6757 1.47 - 1.59: 11513 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 26748 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 26743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 35253 1.72 - 3.44: 1064 3.44 - 5.16: 90 5.16 - 6.88: 19 6.88 - 8.60: 3 Bond angle restraints: 36429 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 112.29 106.77 5.52 9.40e-01 1.13e+00 3.44e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" N VAL C 722 " pdb=" CA VAL C 722 " pdb=" C VAL C 722 " ideal model delta sigma weight residual 113.71 110.60 3.11 9.50e-01 1.11e+00 1.07e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 120.53 -6.13 2.30e+00 1.89e-01 7.11e+00 ... (remaining 36424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15050 17.47 - 34.95: 1269 34.95 - 52.42: 225 52.42 - 69.89: 68 69.89 - 87.37: 27 Dihedral angle restraints: 16639 sinusoidal: 7158 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -0.49 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.96 -80.04 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 742 " pdb=" CB CYS B 742 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 16636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3831 0.079 - 0.159: 440 0.159 - 0.238: 12 0.238 - 0.318: 6 0.318 - 0.397: 4 Chirality restraints: 4293 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 4290 not shown) Planarity restraints: 4697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 664 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B 665 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.031 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN B 603 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B1049 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B1050 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B1050 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1050 " -0.033 5.00e-02 4.00e+02 ... (remaining 4694 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 424 2.64 - 3.20: 25246 3.20 - 3.77: 39970 3.77 - 4.33: 54712 4.33 - 4.90: 87006 Nonbonded interactions: 207358 Sorted by model distance: nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.071 3.040 nonbonded pdb=" OG SER B 751 " pdb=" OG1 THR B 754 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.140 3.040 nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.143 3.040 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.156 3.040 ... (remaining 207353 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 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1310)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1310)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 26.160 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26844 Z= 0.197 Angle : 0.710 11.087 36678 Z= 0.372 Chirality : 0.048 0.397 4293 Planarity : 0.005 0.103 4653 Dihedral : 13.403 87.365 10432 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3239 helix: 0.61 (0.21), residues: 645 sheet: -1.12 (0.20), residues: 636 loop : -2.19 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 355 TYR 0.019 0.001 TYR A 866 PHE 0.035 0.002 PHE C 392 TRP 0.022 0.001 TRP C 436 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00406 (26748) covalent geometry : angle 0.67443 (36429) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.92737 ( 78) hydrogen bonds : bond 0.13690 ( 899) hydrogen bonds : angle 7.28067 ( 2499) link_BETA1-4 : bond 0.00566 ( 13) link_BETA1-4 : angle 2.62092 ( 39) link_NAG-ASN : bond 0.00568 ( 44) link_NAG-ASN : angle 3.20162 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.5670 (mtt180) cc_final: 0.5417 (mtt180) REVERT: A 237 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7980 (mtp85) REVERT: A 516 GLU cc_start: 0.7566 (pm20) cc_final: 0.7347 (pm20) REVERT: C 700 TYR cc_start: 0.8375 (t80) cc_final: 0.8092 (t80) REVERT: C 848 PHE cc_start: 0.6649 (t80) cc_final: 0.6397 (t80) REVERT: C 1043 MET cc_start: 0.7802 (ptp) cc_final: 0.7483 (ptp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1383 time to fit residues: 59.4533 Evaluate side-chains 154 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 239 GLN A 865 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS B1094 HIS C 894 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079115 restraints weight = 87196.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079345 restraints weight = 70009.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080082 restraints weight = 52502.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080289 restraints weight = 45354.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080468 restraints weight = 40050.177| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26844 Z= 0.119 Angle : 0.606 10.794 36678 Z= 0.308 Chirality : 0.046 0.369 4293 Planarity : 0.004 0.071 4653 Dihedral : 7.469 59.903 4690 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3239 helix: 0.99 (0.21), residues: 669 sheet: -0.94 (0.20), residues: 647 loop : -2.01 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 993 TYR 0.018 0.001 TYR A1060 PHE 0.023 0.001 PHE B 275 TRP 0.015 0.001 TRP C 436 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00259 (26748) covalent geometry : angle 0.57585 (36429) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.37053 ( 78) hydrogen bonds : bond 0.04367 ( 899) hydrogen bonds : angle 6.04299 ( 2499) link_BETA1-4 : bond 0.00718 ( 13) link_BETA1-4 : angle 2.26211 ( 39) link_NAG-ASN : bond 0.00583 ( 44) link_NAG-ASN : angle 2.81420 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8269 (mtt180) cc_final: 0.8054 (mtp85) REVERT: A 402 ILE cc_start: 0.9016 (pt) cc_final: 0.8750 (tt) REVERT: A 490 PHE cc_start: 0.7574 (t80) cc_final: 0.7212 (t80) REVERT: C 392 PHE cc_start: 0.7827 (m-10) cc_final: 0.7485 (m-80) REVERT: C 849 ASN cc_start: 0.8642 (m110) cc_final: 0.8438 (m110) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.1412 time to fit residues: 59.5012 Evaluate side-chains 164 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 117 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 255 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 563 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 ASN C 958 GLN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.098925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077945 restraints weight = 88623.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077927 restraints weight = 71583.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078440 restraints weight = 58237.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078649 restraints weight = 50736.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078836 restraints weight = 44307.298| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26844 Z= 0.180 Angle : 0.629 10.696 36678 Z= 0.319 Chirality : 0.046 0.379 4293 Planarity : 0.004 0.065 4653 Dihedral : 7.199 59.938 4690 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 3239 helix: 1.02 (0.21), residues: 662 sheet: -0.91 (0.20), residues: 655 loop : -2.03 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.022 0.001 TYR A1060 PHE 0.020 0.001 PHE B 374 TRP 0.018 0.001 TRP B 879 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00401 (26748) covalent geometry : angle 0.60030 (36429) SS BOND : bond 0.00479 ( 39) SS BOND : angle 1.48023 ( 78) hydrogen bonds : bond 0.04413 ( 899) hydrogen bonds : angle 5.93788 ( 2499) link_BETA1-4 : bond 0.00631 ( 13) link_BETA1-4 : angle 2.28231 ( 39) link_NAG-ASN : bond 0.00538 ( 44) link_NAG-ASN : angle 2.75787 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6681 (ptp) cc_final: 0.6306 (ptp) REVERT: A 983 GLU cc_start: 0.6584 (tm-30) cc_final: 0.6019 (tp30) REVERT: C 317 ASN cc_start: 0.8183 (t0) cc_final: 0.7859 (t0) REVERT: C 402 ILE cc_start: 0.8568 (mm) cc_final: 0.8358 (mm) REVERT: C 571 ASP cc_start: 0.7544 (t70) cc_final: 0.7223 (t0) REVERT: C 998 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7920 (mm-40) outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.1379 time to fit residues: 55.2785 Evaluate side-chains 157 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 80 optimal weight: 8.9990 chunk 263 optimal weight: 0.0030 chunk 70 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.100894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080590 restraints weight = 86961.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080350 restraints weight = 71908.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080817 restraints weight = 61240.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081043 restraints weight = 53142.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081265 restraints weight = 45279.648| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26844 Z= 0.114 Angle : 0.587 10.155 36678 Z= 0.297 Chirality : 0.045 0.365 4293 Planarity : 0.004 0.056 4653 Dihedral : 6.769 58.902 4690 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 3239 helix: 1.20 (0.21), residues: 663 sheet: -0.79 (0.20), residues: 656 loop : -1.98 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1012 TYR 0.017 0.001 TYR A1060 PHE 0.023 0.001 PHE B 201 TRP 0.012 0.001 TRP A 633 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00252 (26748) covalent geometry : angle 0.56021 (36429) SS BOND : bond 0.00448 ( 39) SS BOND : angle 1.39031 ( 78) hydrogen bonds : bond 0.03932 ( 899) hydrogen bonds : angle 5.69784 ( 2499) link_BETA1-4 : bond 0.00712 ( 13) link_BETA1-4 : angle 2.25115 ( 39) link_NAG-ASN : bond 0.00546 ( 44) link_NAG-ASN : angle 2.56610 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6670 (ptp) cc_final: 0.6352 (ptp) REVERT: A 490 PHE cc_start: 0.7537 (t80) cc_final: 0.7310 (t80) REVERT: A 881 PHE cc_start: 0.8287 (p90) cc_final: 0.8048 (p90) REVERT: B 723 SER cc_start: 0.9080 (t) cc_final: 0.8666 (t) REVERT: B 767 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8743 (mm-40) REVERT: B 770 ASN cc_start: 0.8766 (m-40) cc_final: 0.8558 (m-40) REVERT: B 1040 TYR cc_start: 0.8036 (m-80) cc_final: 0.7729 (m-80) REVERT: B 1044 SER cc_start: 0.8770 (m) cc_final: 0.8453 (p) REVERT: C 317 ASN cc_start: 0.8196 (t0) cc_final: 0.7650 (t0) REVERT: C 402 ILE cc_start: 0.8411 (mm) cc_final: 0.8188 (mm) REVERT: C 571 ASP cc_start: 0.7515 (t70) cc_final: 0.7121 (t0) REVERT: C 754 THR cc_start: 0.7868 (p) cc_final: 0.7518 (t) REVERT: C 767 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8561 (mm-40) REVERT: C 770 ASN cc_start: 0.8924 (m-40) cc_final: 0.8625 (m-40) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.1365 time to fit residues: 61.0356 Evaluate side-chains 161 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 69 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.098833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077953 restraints weight = 87747.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077727 restraints weight = 76083.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078310 restraints weight = 60079.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078664 restraints weight = 49019.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078765 restraints weight = 44095.359| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26844 Z= 0.187 Angle : 0.629 9.982 36678 Z= 0.318 Chirality : 0.046 0.377 4293 Planarity : 0.004 0.059 4653 Dihedral : 6.802 59.049 4690 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.15), residues: 3239 helix: 1.02 (0.21), residues: 668 sheet: -0.82 (0.20), residues: 704 loop : -1.96 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.021 0.001 TYR A1060 PHE 0.019 0.001 PHE B 899 TRP 0.017 0.001 TRP A 104 HIS 0.020 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00424 (26748) covalent geometry : angle 0.60230 (36429) SS BOND : bond 0.00422 ( 39) SS BOND : angle 1.70266 ( 78) hydrogen bonds : bond 0.04185 ( 899) hydrogen bonds : angle 5.72128 ( 2499) link_BETA1-4 : bond 0.00629 ( 13) link_BETA1-4 : angle 2.26866 ( 39) link_NAG-ASN : bond 0.00472 ( 44) link_NAG-ASN : angle 2.54957 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.7619 (t80) cc_final: 0.7379 (t80) REVERT: C 317 ASN cc_start: 0.7880 (t0) cc_final: 0.7373 (t0) REVERT: C 402 ILE cc_start: 0.8460 (mm) cc_final: 0.8228 (mm) REVERT: C 571 ASP cc_start: 0.7558 (t70) cc_final: 0.7208 (t0) REVERT: C 754 THR cc_start: 0.7886 (p) cc_final: 0.7630 (t) REVERT: C 998 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 1043 MET cc_start: 0.8391 (ptp) cc_final: 0.7911 (ptp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1369 time to fit residues: 55.8753 Evaluate side-chains 150 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 182 optimal weight: 0.3980 chunk 317 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 310 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079232 restraints weight = 87046.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079588 restraints weight = 69412.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080077 restraints weight = 51792.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080476 restraints weight = 43282.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080537 restraints weight = 39538.451| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26844 Z= 0.124 Angle : 0.596 10.555 36678 Z= 0.300 Chirality : 0.046 0.367 4293 Planarity : 0.004 0.052 4653 Dihedral : 6.595 59.988 4690 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.16 % 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: -1.46 (0.15), residues: 3239 helix: 1.12 (0.21), residues: 671 sheet: -0.75 (0.20), residues: 666 loop : -1.92 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 976 TYR 0.022 0.001 TYR B 897 PHE 0.022 0.001 PHE C 392 TRP 0.021 0.001 TRP B 879 HIS 0.015 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00285 (26748) covalent geometry : angle 0.56752 (36429) SS BOND : bond 0.00406 ( 39) SS BOND : angle 1.49989 ( 78) hydrogen bonds : bond 0.03965 ( 899) hydrogen bonds : angle 5.58116 ( 2499) link_BETA1-4 : bond 0.00676 ( 13) link_BETA1-4 : angle 2.26040 ( 39) link_NAG-ASN : bond 0.00507 ( 44) link_NAG-ASN : angle 2.61675 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1044 SER cc_start: 0.8811 (m) cc_final: 0.8497 (p) REVERT: C 317 ASN cc_start: 0.7894 (t0) cc_final: 0.7455 (t0) REVERT: C 402 ILE cc_start: 0.8408 (mm) cc_final: 0.8177 (mm) REVERT: C 571 ASP cc_start: 0.7434 (t70) cc_final: 0.7052 (t0) REVERT: C 770 ASN cc_start: 0.8939 (m-40) cc_final: 0.8594 (m-40) REVERT: C 998 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7753 (mm-40) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1380 time to fit residues: 59.7897 Evaluate side-chains 158 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 0.0170 chunk 180 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 0.0370 chunk 158 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN C 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.101672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080736 restraints weight = 87093.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081211 restraints weight = 67729.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081590 restraints weight = 51350.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081864 restraints weight = 45472.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081988 restraints weight = 40974.083| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 26844 Z= 0.108 Angle : 0.586 9.664 36678 Z= 0.296 Chirality : 0.045 0.358 4293 Planarity : 0.004 0.049 4653 Dihedral : 6.324 59.713 4690 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3239 helix: 1.27 (0.21), residues: 671 sheet: -0.53 (0.21), residues: 606 loop : -1.87 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 190 TYR 0.016 0.001 TYR A 204 PHE 0.033 0.001 PHE B 374 TRP 0.013 0.001 TRP C 436 HIS 0.011 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00244 (26748) covalent geometry : angle 0.55924 (36429) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.62689 ( 78) hydrogen bonds : bond 0.03779 ( 899) hydrogen bonds : angle 5.40319 ( 2499) link_BETA1-4 : bond 0.00684 ( 13) link_BETA1-4 : angle 2.22785 ( 39) link_NAG-ASN : bond 0.00530 ( 44) link_NAG-ASN : angle 2.47046 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6574 (ptp) cc_final: 0.6242 (ptp) REVERT: A 983 GLU cc_start: 0.6834 (tp30) cc_final: 0.5701 (tp30) REVERT: B 1044 SER cc_start: 0.8840 (m) cc_final: 0.8476 (p) REVERT: C 317 ASN cc_start: 0.7970 (t0) cc_final: 0.7421 (t0) REVERT: C 402 ILE cc_start: 0.8302 (mm) cc_final: 0.8059 (mm) REVERT: C 534 VAL cc_start: 0.8351 (t) cc_final: 0.8041 (t) REVERT: C 552 LEU cc_start: 0.9075 (mm) cc_final: 0.8484 (mp) REVERT: C 571 ASP cc_start: 0.7361 (t70) cc_final: 0.7042 (t0) REVERT: C 767 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8555 (mm-40) REVERT: C 770 ASN cc_start: 0.8751 (m-40) cc_final: 0.8535 (m-40) REVERT: C 998 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7658 (mm-40) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1418 time to fit residues: 63.1710 Evaluate side-chains 168 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 318 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078469 restraints weight = 88298.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078295 restraints weight = 77189.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078912 restraints weight = 59639.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079292 restraints weight = 47739.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079366 restraints weight = 43547.602| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 26844 Z= 0.185 Angle : 0.640 9.837 36678 Z= 0.323 Chirality : 0.046 0.364 4293 Planarity : 0.004 0.057 4653 Dihedral : 6.526 58.844 4690 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3239 helix: 0.93 (0.21), residues: 683 sheet: -0.64 (0.20), residues: 682 loop : -1.88 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.019 0.001 TYR A1060 PHE 0.033 0.002 PHE B 816 TRP 0.013 0.001 TRP C 436 HIS 0.011 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00421 (26748) covalent geometry : angle 0.61182 (36429) SS BOND : bond 0.00390 ( 39) SS BOND : angle 1.93147 ( 78) hydrogen bonds : bond 0.04171 ( 899) hydrogen bonds : angle 5.55891 ( 2499) link_BETA1-4 : bond 0.00628 ( 13) link_BETA1-4 : angle 2.26392 ( 39) link_NAG-ASN : bond 0.00488 ( 44) link_NAG-ASN : angle 2.58179 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8981 (pt) cc_final: 0.8736 (tt) REVERT: A 692 LEU cc_start: 0.8866 (mt) cc_final: 0.8605 (mt) REVERT: A 983 GLU cc_start: 0.6822 (tp30) cc_final: 0.6590 (tp30) REVERT: B 1044 SER cc_start: 0.8832 (m) cc_final: 0.8525 (p) REVERT: C 317 ASN cc_start: 0.8023 (t0) cc_final: 0.7582 (t0) REVERT: C 534 VAL cc_start: 0.8474 (t) cc_final: 0.8245 (t) REVERT: C 552 LEU cc_start: 0.9083 (mm) cc_final: 0.8484 (mp) REVERT: C 571 ASP cc_start: 0.7440 (t70) cc_final: 0.7110 (t0) REVERT: C 770 ASN cc_start: 0.8925 (m-40) cc_final: 0.8616 (m-40) REVERT: C 998 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7893 (mm-40) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1386 time to fit residues: 56.7468 Evaluate side-chains 155 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 114 optimal weight: 0.0000 chunk 9 optimal weight: 6.9990 chunk 260 optimal weight: 0.0370 chunk 210 optimal weight: 5.9990 overall best weight: 1.9866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN C 894 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 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 = 0.3744 r_free = 0.3744 target = 0.099776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078942 restraints weight = 87959.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078691 restraints weight = 77586.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079177 restraints weight = 60917.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079681 restraints weight = 48367.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079756 restraints weight = 42809.609| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 26844 Z= 0.156 Angle : 0.624 9.923 36678 Z= 0.316 Chirality : 0.046 0.384 4293 Planarity : 0.004 0.052 4653 Dihedral : 6.519 59.251 4690 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3239 helix: 1.08 (0.21), residues: 670 sheet: -0.59 (0.20), residues: 671 loop : -1.89 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.019 0.001 TYR A1060 PHE 0.029 0.002 PHE B 201 TRP 0.014 0.001 TRP C 436 HIS 0.010 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00360 (26748) covalent geometry : angle 0.59616 (36429) SS BOND : bond 0.00373 ( 39) SS BOND : angle 1.91795 ( 78) hydrogen bonds : bond 0.04052 ( 899) hydrogen bonds : angle 5.52477 ( 2499) link_BETA1-4 : bond 0.00668 ( 13) link_BETA1-4 : angle 2.25744 ( 39) link_NAG-ASN : bond 0.00475 ( 44) link_NAG-ASN : angle 2.51346 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6544 (ptp) cc_final: 0.6227 (ptp) REVERT: A 402 ILE cc_start: 0.9000 (pt) cc_final: 0.8785 (tt) REVERT: A 983 GLU cc_start: 0.6795 (tp30) cc_final: 0.6554 (tp30) REVERT: C 223 LEU cc_start: 0.9052 (tp) cc_final: 0.8790 (tp) REVERT: C 317 ASN cc_start: 0.8127 (t0) cc_final: 0.7545 (t0) REVERT: C 534 VAL cc_start: 0.8481 (t) cc_final: 0.8186 (t) REVERT: C 552 LEU cc_start: 0.9131 (mm) cc_final: 0.8520 (mp) REVERT: C 571 ASP cc_start: 0.7434 (t70) cc_final: 0.7093 (t0) REVERT: C 767 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8573 (mm-40) REVERT: C 770 ASN cc_start: 0.8895 (m-40) cc_final: 0.8615 (m-40) REVERT: C 981 GLU cc_start: 0.7593 (mp0) cc_final: 0.6838 (mt-10) REVERT: C 998 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7822 (mm-40) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1389 time to fit residues: 57.7925 Evaluate side-chains 158 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 173 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 213 optimal weight: 0.0170 chunk 47 optimal weight: 0.2980 chunk 183 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN C 564 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079350 restraints weight = 87470.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078924 restraints weight = 75121.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079630 restraints weight = 59412.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079801 restraints weight = 53204.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080053 restraints weight = 43686.594| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 26844 Z= 0.133 Angle : 0.604 9.610 36678 Z= 0.306 Chirality : 0.046 0.372 4293 Planarity : 0.004 0.051 4653 Dihedral : 6.388 59.227 4690 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.36 (0.15), residues: 3239 helix: 1.11 (0.21), residues: 672 sheet: -0.50 (0.21), residues: 647 loop : -1.89 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 993 TYR 0.025 0.001 TYR B 897 PHE 0.030 0.001 PHE A 275 TRP 0.026 0.001 TRP B 879 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00311 (26748) covalent geometry : angle 0.57734 (36429) SS BOND : bond 0.00361 ( 39) SS BOND : angle 1.82203 ( 78) hydrogen bonds : bond 0.03919 ( 899) hydrogen bonds : angle 5.46386 ( 2499) link_BETA1-4 : bond 0.00628 ( 13) link_BETA1-4 : angle 2.24124 ( 39) link_NAG-ASN : bond 0.00483 ( 44) link_NAG-ASN : angle 2.44131 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.9039 (pt) cc_final: 0.8828 (tt) REVERT: A 983 GLU cc_start: 0.6798 (tp30) cc_final: 0.6551 (tp30) REVERT: B 1040 TYR cc_start: 0.8099 (m-80) cc_final: 0.7720 (m-80) REVERT: B 1044 SER cc_start: 0.8727 (m) cc_final: 0.8292 (p) REVERT: C 223 LEU cc_start: 0.9012 (tp) cc_final: 0.8780 (tp) REVERT: C 317 ASN cc_start: 0.7981 (t0) cc_final: 0.7625 (t0) REVERT: C 534 VAL cc_start: 0.8507 (t) cc_final: 0.8248 (t) REVERT: C 552 LEU cc_start: 0.9130 (mm) cc_final: 0.8565 (mp) REVERT: C 571 ASP cc_start: 0.7338 (t70) cc_final: 0.7035 (t0) REVERT: C 767 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8569 (mm-40) REVERT: C 981 GLU cc_start: 0.7591 (mp0) cc_final: 0.6892 (mt-10) REVERT: C 998 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7716 (mm-40) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1391 time to fit residues: 57.9513 Evaluate side-chains 164 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 86 optimal weight: 0.5980 chunk 235 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** 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 = 0.3775 r_free = 0.3775 target = 0.101454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080711 restraints weight = 87058.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080924 restraints weight = 75306.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081387 restraints weight = 58329.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081865 restraints weight = 47218.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081944 restraints weight = 41254.733| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 26844 Z= 0.112 Angle : 0.590 9.452 36678 Z= 0.298 Chirality : 0.045 0.366 4293 Planarity : 0.004 0.048 4653 Dihedral : 6.215 59.658 4690 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 3239 helix: 1.25 (0.21), residues: 673 sheet: -0.43 (0.21), residues: 629 loop : -1.82 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1032 TYR 0.018 0.001 TYR B 866 PHE 0.026 0.001 PHE A 275 TRP 0.014 0.001 TRP C 436 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00256 (26748) covalent geometry : angle 0.56439 (36429) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.68496 ( 78) hydrogen bonds : bond 0.03766 ( 899) hydrogen bonds : angle 5.35176 ( 2499) link_BETA1-4 : bond 0.00667 ( 13) link_BETA1-4 : angle 2.20975 ( 39) link_NAG-ASN : bond 0.00524 ( 44) link_NAG-ASN : angle 2.36211 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.53 seconds wall clock time: 59 minutes 2.63 seconds (3542.63 seconds total)