Starting phenix.real_space_refine on Fri Mar 6 01:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru2_24694/03_2026/7ru2_24694.map" } resolution = 3.0 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= 0.029 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 126 5.16 5 C 16921 2.51 5 N 4375 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s 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: 26646 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8608 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 3 Chain: "B" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8585 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8585 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 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: "Q" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.89, per 1000 atoms: 0.22 Number of scatterers: 26646 At special positions: 0 Unit cell: (144.2, 156.56, 179.22, 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 126 16.00 O 5224 8.00 N 4375 7.00 C 16921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.16 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS C 883 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.11 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 149 " " NAG C1311 " - " ASN C 165 " " NAG C1312 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6172 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 58 sheets defined 27.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.735A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.777A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.873A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.946A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.879A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.902A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.270A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.734A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.923A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.546A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 847 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.964A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.515A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.739A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.611A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.142A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.573A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.911A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.830A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.670A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.670A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.812A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.326A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.583A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.450A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.579A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.418A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.426A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.537A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.827A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.565A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.046A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 4.702A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.906A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.319A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.461A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.521A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.580A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.114A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.056A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.410A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.679A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.416A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.996A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.829A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.826A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.373A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF1, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.630A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.470A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.566A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.475A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.448A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.918A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.035A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.742A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3066 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: 6.56 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5597 1.32 - 1.47: 10269 1.47 - 1.62: 11228 1.62 - 1.77: 35 1.77 - 1.92: 121 Bond restraints: 27250 Sorted by residual: bond pdb=" CB HIS B 66 " pdb=" CG HIS B 66 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.32e+01 bond pdb=" CB ASN A1135 " pdb=" CG ASN A1135 " ideal model delta sigma weight residual 1.516 1.371 0.145 2.50e-02 1.60e+03 3.36e+01 bond pdb=" CB PHE C 888 " pdb=" CG PHE C 888 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.13e+01 bond pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 1.502 1.378 0.124 2.30e-02 1.89e+03 2.92e+01 bond pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 1.502 1.378 0.124 2.30e-02 1.89e+03 2.89e+01 ... (remaining 27245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.56: 37001 7.56 - 15.12: 81 15.12 - 22.68: 0 22.68 - 30.24: 0 30.24 - 37.80: 4 Bond angle restraints: 37086 Sorted by residual: angle pdb=" C2 NAG B1311 " pdb=" N2 NAG B1311 " pdb=" C7 NAG B1311 " ideal model delta sigma weight residual 124.56 162.36 -37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG C1309 " pdb=" N2 NAG C1309 " pdb=" C7 NAG C1309 " ideal model delta sigma weight residual 124.56 159.84 -35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C2 NAG A1305 " pdb=" N2 NAG A1305 " pdb=" C7 NAG A1305 " ideal model delta sigma weight residual 124.56 159.00 -34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C2 NAG C1306 " pdb=" N2 NAG C1306 " pdb=" C7 NAG C1306 " ideal model delta sigma weight residual 124.56 158.75 -34.19 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 119.85 128.44 -8.59 1.01e+00 9.80e-01 7.23e+01 ... (remaining 37081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 16460 17.75 - 35.50: 428 35.50 - 53.25: 118 53.25 - 71.00: 42 71.00 - 88.75: 22 Dihedral angle restraints: 17070 sinusoidal: 7467 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS C 705 " pdb=" CB CYS C 705 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 163.04 -70.04 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" C CYS B 166 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " ideal model delta harmonic sigma weight residual -122.60 -131.99 9.39 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 17067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3046 0.103 - 0.205: 963 0.205 - 0.308: 223 0.308 - 0.411: 88 0.411 - 0.513: 43 Chirality restraints: 4363 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 4360 not shown) Planarity restraints: 4781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.064 2.00e-02 2.50e+03 6.87e-02 5.90e+01 pdb=" CG ASN C 709 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.061 2.00e-02 2.50e+03 6.26e-02 4.90e+01 pdb=" CG ASN B 61 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.059 2.00e-02 2.50e+03 5.88e-02 4.32e+01 pdb=" CG ASN A 343 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 4778 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 10640 2.89 - 3.39: 24146 3.39 - 3.90: 44985 3.90 - 4.40: 52723 4.40 - 4.90: 85667 Nonbonded interactions: 218161 Sorted by model distance: nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.391 2.496 nonbonded pdb=" OE1 GLU C 340 " pdb=" NZ LYS C 356 " model vdw 2.401 3.120 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.402 2.496 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.412 3.120 nonbonded pdb=" OE1 GLU B 340 " pdb=" NZ LYS B 356 " model vdw 2.425 3.120 ... (remaining 218156 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 14 through 71 or resid 76 through 1311)) selection = chain 'B' selection = (chain 'C' and resid 14 through 1311) } 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' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.350 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.730 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.022 0.145 27360 Z= 1.159 Angle : 1.799 37.805 37368 Z= 1.179 Chirality : 0.121 0.513 4363 Planarity : 0.008 0.048 4733 Dihedral : 9.886 88.754 10754 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.14 % Allowed : 0.31 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3273 helix: 0.30 (0.17), residues: 751 sheet: 1.21 (0.19), residues: 690 loop : 0.18 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 509 TYR 0.063 0.008 TYR A 266 PHE 0.039 0.005 PHE A 58 TRP 0.038 0.008 TRP B 633 HIS 0.013 0.003 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.02163 (27250) covalent geometry : angle 1.78739 (37086) SS BOND : bond 0.02760 ( 48) SS BOND : angle 2.59575 ( 96) hydrogen bonds : bond 0.17315 ( 1117) hydrogen bonds : angle 7.90694 ( 3066) link_BETA1-4 : bond 0.06990 ( 14) link_BETA1-4 : angle 4.86813 ( 42) link_NAG-ASN : bond 0.08127 ( 48) link_NAG-ASN : angle 2.30910 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 289 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7863 (t0) cc_final: 0.7611 (t0) REVERT: A 76 THR cc_start: 0.8155 (m) cc_final: 0.7824 (p) REVERT: A 420 ASP cc_start: 0.8236 (m-30) cc_final: 0.7982 (m-30) REVERT: A 571 ASP cc_start: 0.8405 (t0) cc_final: 0.8146 (t0) REVERT: A 843 ASP cc_start: 0.6962 (t70) cc_final: 0.6644 (t0) REVERT: A 867 ASP cc_start: 0.8135 (m-30) cc_final: 0.7833 (m-30) REVERT: B 177 MET cc_start: 0.6219 (ttp) cc_final: 0.5851 (ttp) REVERT: B 596 SER cc_start: 0.9296 (p) cc_final: 0.9046 (m) REVERT: B 748 GLU cc_start: 0.8298 (mp0) cc_final: 0.8070 (mp0) REVERT: C 61 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7417 (t0) REVERT: C 197 ILE cc_start: 0.8703 (mt) cc_final: 0.8448 (pp) outliers start: 4 outliers final: 2 residues processed: 293 average time/residue: 0.7661 time to fit residues: 254.6491 Evaluate side-chains 103 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN A 188 ASN B 66 HIS B 115 GLN B 188 ASN B 218 GLN B 784 GLN B1010 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 52 GLN C 137 ASN C 836 GLN C 955 ASN C1010 GLN C1011 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069729 restraints weight = 62122.236| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.99 r_work: 0.3121 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27360 Z= 0.164 Angle : 0.719 14.554 37368 Z= 0.375 Chirality : 0.047 0.218 4363 Planarity : 0.004 0.047 4733 Dihedral : 6.079 57.752 4853 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 1.73 % Allowed : 4.55 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3273 helix: 1.69 (0.19), residues: 748 sheet: 0.87 (0.19), residues: 717 loop : -0.23 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 466 TYR 0.033 0.002 TYR B 495 PHE 0.023 0.002 PHE B 497 TRP 0.013 0.001 TRP B 633 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00348 (27250) covalent geometry : angle 0.69223 (37086) SS BOND : bond 0.00426 ( 48) SS BOND : angle 1.70363 ( 96) hydrogen bonds : bond 0.06266 ( 1117) hydrogen bonds : angle 6.44168 ( 3066) link_BETA1-4 : bond 0.00457 ( 14) link_BETA1-4 : angle 2.81146 ( 42) link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 2.53694 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: A 53 ASP cc_start: 0.8479 (t0) cc_final: 0.7997 (t0) REVERT: A 177 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7343 (ttm) REVERT: A 420 ASP cc_start: 0.8448 (m-30) cc_final: 0.8153 (m-30) REVERT: A 571 ASP cc_start: 0.8593 (t0) cc_final: 0.8227 (t0) REVERT: A 577 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8036 (ttp-170) REVERT: A 703 ASN cc_start: 0.8142 (t0) cc_final: 0.7646 (t0) REVERT: A 762 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 823 PHE cc_start: 0.8299 (m-80) cc_final: 0.7719 (m-80) REVERT: A 843 ASP cc_start: 0.7370 (t70) cc_final: 0.6792 (t0) REVERT: A 867 ASP cc_start: 0.8372 (m-30) cc_final: 0.8164 (m-30) REVERT: B 88 ASP cc_start: 0.7988 (t0) cc_final: 0.7731 (t0) REVERT: B 177 MET cc_start: 0.6186 (ttp) cc_final: 0.5801 (ttp) REVERT: C 153 MET cc_start: 0.7961 (mtp) cc_final: 0.7679 (mtp) REVERT: C 346 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7613 (ttm-80) REVERT: C 675 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: C 1019 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8068 (tpm170) outliers start: 50 outliers final: 10 residues processed: 176 average time/residue: 0.6408 time to fit residues: 131.6742 Evaluate side-chains 109 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 50 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 284 optimal weight: 0.4980 chunk 276 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A1002 GLN B 52 GLN B 66 HIS B 115 GLN C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067144 restraints weight = 62623.047| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.99 r_work: 0.3070 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27360 Z= 0.177 Angle : 0.629 9.540 37368 Z= 0.328 Chirality : 0.046 0.254 4363 Planarity : 0.004 0.044 4733 Dihedral : 5.582 56.753 4849 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 1.42 % Allowed : 6.04 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3273 helix: 1.93 (0.19), residues: 744 sheet: 0.63 (0.18), residues: 773 loop : -0.40 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.020 0.001 TYR B 265 PHE 0.028 0.002 PHE B 927 TRP 0.013 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00412 (27250) covalent geometry : angle 0.60823 (37086) SS BOND : bond 0.00231 ( 48) SS BOND : angle 1.52399 ( 96) hydrogen bonds : bond 0.05586 ( 1117) hydrogen bonds : angle 5.97929 ( 3066) link_BETA1-4 : bond 0.00538 ( 14) link_BETA1-4 : angle 1.96064 ( 42) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 2.18845 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: A 53 ASP cc_start: 0.8557 (t0) cc_final: 0.8039 (t0) REVERT: A 68 ILE cc_start: 0.8919 (tt) cc_final: 0.8213 (mp) REVERT: A 177 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7338 (ttm) REVERT: A 378 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8185 (pttp) REVERT: A 420 ASP cc_start: 0.8646 (m-30) cc_final: 0.8368 (m-30) REVERT: A 577 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7986 (ttp-170) REVERT: A 703 ASN cc_start: 0.8234 (t0) cc_final: 0.7797 (t0) REVERT: A 823 PHE cc_start: 0.8279 (m-80) cc_final: 0.7765 (m-80) REVERT: A 843 ASP cc_start: 0.7250 (t70) cc_final: 0.6774 (t0) REVERT: B 88 ASP cc_start: 0.7977 (t0) cc_final: 0.7698 (t0) REVERT: B 773 GLU cc_start: 0.8111 (tt0) cc_final: 0.7837 (tt0) REVERT: B 985 ASP cc_start: 0.7604 (p0) cc_final: 0.7331 (p0) REVERT: C 153 MET cc_start: 0.8052 (mtp) cc_final: 0.7790 (mtp) REVERT: C 320 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8802 (m) REVERT: C 675 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: C 1019 ARG cc_start: 0.8457 (ttp-110) cc_final: 0.8135 (tpm170) outliers start: 41 outliers final: 17 residues processed: 145 average time/residue: 0.6599 time to fit residues: 111.1826 Evaluate side-chains 114 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 169 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 300 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.083212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.068056 restraints weight = 61536.499| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.87 r_work: 0.3095 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27360 Z= 0.123 Angle : 0.555 9.594 37368 Z= 0.289 Chirality : 0.044 0.245 4363 Planarity : 0.004 0.047 4733 Dihedral : 5.218 56.528 4849 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.98 % Rotamer: Outliers : 1.08 % Allowed : 7.04 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3273 helix: 2.06 (0.19), residues: 740 sheet: 0.46 (0.18), residues: 783 loop : -0.47 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.020 0.001 TYR B 265 PHE 0.023 0.001 PHE B 823 TRP 0.010 0.001 TRP A 152 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00272 (27250) covalent geometry : angle 0.53739 (37086) SS BOND : bond 0.00196 ( 48) SS BOND : angle 1.35430 ( 96) hydrogen bonds : bond 0.04766 ( 1117) hydrogen bonds : angle 5.71652 ( 3066) link_BETA1-4 : bond 0.00450 ( 14) link_BETA1-4 : angle 1.66332 ( 42) link_NAG-ASN : bond 0.00337 ( 48) link_NAG-ASN : angle 1.85601 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 53 ASP cc_start: 0.8574 (t0) cc_final: 0.8038 (t0) REVERT: A 76 THR cc_start: 0.8058 (m) cc_final: 0.7685 (t) REVERT: A 177 MET cc_start: 0.7767 (ttp) cc_final: 0.7296 (ttm) REVERT: A 378 LYS cc_start: 0.8552 (ptpp) cc_final: 0.8228 (pttp) REVERT: A 420 ASP cc_start: 0.8622 (m-30) cc_final: 0.8325 (m-30) REVERT: A 703 ASN cc_start: 0.8198 (t0) cc_final: 0.7787 (t0) REVERT: A 843 ASP cc_start: 0.7310 (t70) cc_final: 0.6846 (t0) REVERT: B 40 ASP cc_start: 0.8118 (t0) cc_final: 0.7893 (p0) REVERT: B 88 ASP cc_start: 0.7922 (t0) cc_final: 0.7639 (t0) REVERT: B 773 GLU cc_start: 0.8085 (tt0) cc_final: 0.7849 (tt0) REVERT: C 153 MET cc_start: 0.8162 (mtp) cc_final: 0.7928 (mtp) REVERT: C 486 PHE cc_start: 0.8295 (t80) cc_final: 0.7476 (t80) REVERT: C 1019 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.7996 (tpm170) outliers start: 31 outliers final: 12 residues processed: 124 average time/residue: 0.6721 time to fit residues: 96.8855 Evaluate side-chains 100 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 265 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 196 ASN A1002 GLN B 613 GLN B1135 ASN C 52 GLN C 245 HIS C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064538 restraints weight = 62809.600| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.97 r_work: 0.3010 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27360 Z= 0.231 Angle : 0.621 9.640 37368 Z= 0.323 Chirality : 0.047 0.261 4363 Planarity : 0.004 0.053 4733 Dihedral : 5.419 57.987 4849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.53 % Allowed : 7.32 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3273 helix: 1.84 (0.19), residues: 763 sheet: 0.32 (0.18), residues: 793 loop : -0.69 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 983 TYR 0.025 0.002 TYR C 756 PHE 0.023 0.002 PHE B 823 TRP 0.013 0.002 TRP C 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00558 (27250) covalent geometry : angle 0.60486 (37086) SS BOND : bond 0.00260 ( 48) SS BOND : angle 1.46453 ( 96) hydrogen bonds : bond 0.05527 ( 1117) hydrogen bonds : angle 5.78672 ( 3066) link_BETA1-4 : bond 0.00357 ( 14) link_BETA1-4 : angle 1.50902 ( 42) link_NAG-ASN : bond 0.00325 ( 48) link_NAG-ASN : angle 1.90853 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8696 (t0) cc_final: 0.8196 (t0) REVERT: A 177 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7285 (ttm) REVERT: A 378 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8271 (pttp) REVERT: B 88 ASP cc_start: 0.8050 (t0) cc_final: 0.7779 (t0) REVERT: C 153 MET cc_start: 0.8246 (mtp) cc_final: 0.8009 (mtp) REVERT: C 320 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8881 (m) REVERT: C 346 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7776 (ttm-80) REVERT: C 486 PHE cc_start: 0.8393 (t80) cc_final: 0.7591 (t80) REVERT: C 1019 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8204 (tpm170) REVERT: C 1050 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8597 (ptt) outliers start: 44 outliers final: 20 residues processed: 120 average time/residue: 0.6371 time to fit residues: 89.9530 Evaluate side-chains 104 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 57 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 306 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B1010 GLN C 52 GLN C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066666 restraints weight = 62497.099| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.97 r_work: 0.3061 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27360 Z= 0.120 Angle : 0.533 9.521 37368 Z= 0.278 Chirality : 0.044 0.251 4363 Planarity : 0.004 0.050 4733 Dihedral : 5.088 56.092 4849 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.27 % Favored : 96.61 % Rotamer: Outliers : 1.01 % Allowed : 7.88 % Favored : 91.12 % 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: 0.33 (0.14), residues: 3273 helix: 2.21 (0.19), residues: 737 sheet: 0.27 (0.18), residues: 785 loop : -0.68 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.018 0.001 TYR B 265 PHE 0.026 0.001 PHE B 823 TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00265 (27250) covalent geometry : angle 0.51837 (37086) SS BOND : bond 0.00183 ( 48) SS BOND : angle 1.29093 ( 96) hydrogen bonds : bond 0.04591 ( 1117) hydrogen bonds : angle 5.58536 ( 3066) link_BETA1-4 : bond 0.00404 ( 14) link_BETA1-4 : angle 1.36111 ( 42) link_NAG-ASN : bond 0.00297 ( 48) link_NAG-ASN : angle 1.69670 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8722 (t0) cc_final: 0.8146 (t0) REVERT: A 76 THR cc_start: 0.8093 (m) cc_final: 0.7713 (t) REVERT: A 177 MET cc_start: 0.7691 (ttp) cc_final: 0.7254 (ttm) REVERT: A 378 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8221 (pttp) REVERT: A 703 ASN cc_start: 0.8089 (t0) cc_final: 0.7714 (t0) REVERT: A 790 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7631 (ptpp) REVERT: A 1092 GLU cc_start: 0.8343 (pt0) cc_final: 0.7857 (pm20) REVERT: B 88 ASP cc_start: 0.7947 (t0) cc_final: 0.7703 (t0) REVERT: B 773 GLU cc_start: 0.8126 (tt0) cc_final: 0.7791 (tt0) REVERT: B 934 ILE cc_start: 0.8774 (mm) cc_final: 0.8543 (mp) REVERT: C 153 MET cc_start: 0.8262 (mtp) cc_final: 0.8006 (mtp) REVERT: C 320 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8835 (m) REVERT: C 346 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7771 (ttm-80) REVERT: C 486 PHE cc_start: 0.8399 (t80) cc_final: 0.7688 (t80) REVERT: C 1019 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.7976 (tpt170) outliers start: 29 outliers final: 14 residues processed: 110 average time/residue: 0.6169 time to fit residues: 80.4097 Evaluate side-chains 97 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 312 optimal weight: 0.1980 chunk 212 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 195 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A1002 GLN B 314 GLN B 613 GLN C 23 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.083011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068090 restraints weight = 61256.789| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.84 r_work: 0.3096 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27360 Z= 0.102 Angle : 0.510 9.575 37368 Z= 0.265 Chirality : 0.043 0.249 4363 Planarity : 0.004 0.049 4733 Dihedral : 4.848 56.383 4849 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 1.04 % Allowed : 7.88 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3273 helix: 2.26 (0.19), residues: 748 sheet: 0.35 (0.19), residues: 748 loop : -0.61 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.020 0.001 TYR B 265 PHE 0.030 0.001 PHE C 927 TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00217 (27250) covalent geometry : angle 0.49634 (37086) SS BOND : bond 0.00175 ( 48) SS BOND : angle 1.18633 ( 96) hydrogen bonds : bond 0.04155 ( 1117) hydrogen bonds : angle 5.38890 ( 3066) link_BETA1-4 : bond 0.00413 ( 14) link_BETA1-4 : angle 1.23792 ( 42) link_NAG-ASN : bond 0.00285 ( 48) link_NAG-ASN : angle 1.66885 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8616 (t0) cc_final: 0.8006 (t0) REVERT: A 76 THR cc_start: 0.8123 (m) cc_final: 0.7819 (t) REVERT: A 177 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7278 (ttm) REVERT: A 378 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8225 (pttp) REVERT: A 703 ASN cc_start: 0.8149 (t0) cc_final: 0.7727 (t0) REVERT: A 779 GLN cc_start: 0.8624 (tp40) cc_final: 0.8421 (tm-30) REVERT: A 790 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7625 (ptpp) REVERT: A 900 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: A 1092 GLU cc_start: 0.8330 (pt0) cc_final: 0.7881 (pm20) REVERT: B 88 ASP cc_start: 0.7869 (t0) cc_final: 0.7627 (t0) REVERT: B 773 GLU cc_start: 0.8031 (tt0) cc_final: 0.7727 (tt0) REVERT: C 153 MET cc_start: 0.8239 (mtp) cc_final: 0.8010 (mtp) REVERT: C 346 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7770 (ttm-80) REVERT: C 486 PHE cc_start: 0.8413 (t80) cc_final: 0.7699 (t80) REVERT: C 554 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 1019 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7927 (tpm170) outliers start: 30 outliers final: 15 residues processed: 113 average time/residue: 0.6052 time to fit residues: 80.9075 Evaluate side-chains 103 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 300 optimal weight: 20.0000 chunk 325 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C1005 GLN C1088 HIS C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.079643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064417 restraints weight = 62846.495| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.88 r_work: 0.3014 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27360 Z= 0.217 Angle : 0.593 9.634 37368 Z= 0.308 Chirality : 0.046 0.264 4363 Planarity : 0.004 0.051 4733 Dihedral : 5.219 58.030 4849 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 1.08 % Allowed : 8.19 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3273 helix: 2.10 (0.19), residues: 746 sheet: 0.30 (0.19), residues: 762 loop : -0.81 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1014 TYR 0.024 0.002 TYR C 756 PHE 0.029 0.002 PHE B 927 TRP 0.013 0.002 TRP C 886 HIS 0.009 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00517 (27250) covalent geometry : angle 0.57842 (37086) SS BOND : bond 0.00244 ( 48) SS BOND : angle 1.35940 ( 96) hydrogen bonds : bond 0.05229 ( 1117) hydrogen bonds : angle 5.59291 ( 3066) link_BETA1-4 : bond 0.00338 ( 14) link_BETA1-4 : angle 1.25114 ( 42) link_NAG-ASN : bond 0.00317 ( 48) link_NAG-ASN : angle 1.81259 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8751 (t0) cc_final: 0.8202 (t0) REVERT: A 177 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: A 378 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8210 (pttp) REVERT: A 703 ASN cc_start: 0.8366 (t0) cc_final: 0.7931 (t0) REVERT: A 762 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7667 (mm-40) REVERT: A 779 GLN cc_start: 0.8727 (tp40) cc_final: 0.8471 (tm-30) REVERT: A 790 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7605 (ptpp) REVERT: A 900 MET cc_start: 0.8968 (mtp) cc_final: 0.8725 (mtm) REVERT: A 1092 GLU cc_start: 0.8424 (pt0) cc_final: 0.8043 (pm20) REVERT: B 88 ASP cc_start: 0.8009 (t0) cc_final: 0.7767 (t0) REVERT: C 153 MET cc_start: 0.8325 (mtp) cc_final: 0.8096 (mtp) REVERT: C 486 PHE cc_start: 0.8422 (t80) cc_final: 0.7686 (t80) REVERT: C 1019 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8067 (tpt170) outliers start: 31 outliers final: 16 residues processed: 100 average time/residue: 0.6040 time to fit residues: 71.9217 Evaluate side-chains 98 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 92 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 205 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.081943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066325 restraints weight = 62530.398| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.97 r_work: 0.3052 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27360 Z= 0.119 Angle : 0.530 9.511 37368 Z= 0.275 Chirality : 0.044 0.255 4363 Planarity : 0.004 0.049 4733 Dihedral : 4.985 56.139 4849 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 0.83 % Allowed : 8.57 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3273 helix: 2.31 (0.19), residues: 739 sheet: 0.33 (0.19), residues: 740 loop : -0.77 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.018 0.001 TYR C1067 PHE 0.030 0.001 PHE B 823 TRP 0.008 0.001 TRP A 152 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00269 (27250) covalent geometry : angle 0.51532 (37086) SS BOND : bond 0.00191 ( 48) SS BOND : angle 1.35601 ( 96) hydrogen bonds : bond 0.04503 ( 1117) hydrogen bonds : angle 5.44801 ( 3066) link_BETA1-4 : bond 0.00373 ( 14) link_BETA1-4 : angle 1.15707 ( 42) link_NAG-ASN : bond 0.00280 ( 48) link_NAG-ASN : angle 1.66519 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8679 (t0) cc_final: 0.8066 (t0) REVERT: A 177 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7356 (ttm) REVERT: A 244 LEU cc_start: 0.8105 (mt) cc_final: 0.7871 (pp) REVERT: A 378 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8230 (pttp) REVERT: A 703 ASN cc_start: 0.8305 (t0) cc_final: 0.7903 (t0) REVERT: A 779 GLN cc_start: 0.8696 (tp40) cc_final: 0.8448 (tm-30) REVERT: A 900 MET cc_start: 0.8891 (mtp) cc_final: 0.8627 (mtm) REVERT: A 1092 GLU cc_start: 0.8471 (pt0) cc_final: 0.8077 (pm20) REVERT: B 88 ASP cc_start: 0.7965 (t0) cc_final: 0.7721 (t0) REVERT: C 153 MET cc_start: 0.8366 (mtp) cc_final: 0.8126 (mtp) REVERT: C 486 PHE cc_start: 0.8439 (t80) cc_final: 0.7688 (t80) REVERT: C 1019 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.7986 (tpt170) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 0.6244 time to fit residues: 72.3902 Evaluate side-chains 99 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 46 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.081362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065680 restraints weight = 62636.685| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.97 r_work: 0.3040 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27360 Z= 0.144 Angle : 0.542 9.581 37368 Z= 0.281 Chirality : 0.044 0.257 4363 Planarity : 0.004 0.049 4733 Dihedral : 5.003 57.252 4849 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.90 % Allowed : 8.54 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3273 helix: 2.24 (0.19), residues: 746 sheet: 0.32 (0.19), residues: 754 loop : -0.82 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 346 TYR 0.019 0.001 TYR B 265 PHE 0.031 0.001 PHE B 823 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00336 (27250) covalent geometry : angle 0.52861 (37086) SS BOND : bond 0.00194 ( 48) SS BOND : angle 1.35612 ( 96) hydrogen bonds : bond 0.04619 ( 1117) hydrogen bonds : angle 5.43037 ( 3066) link_BETA1-4 : bond 0.00345 ( 14) link_BETA1-4 : angle 1.16722 ( 42) link_NAG-ASN : bond 0.00274 ( 48) link_NAG-ASN : angle 1.66639 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8711 (t0) cc_final: 0.8100 (t0) REVERT: A 177 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7385 (ttm) REVERT: A 378 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8238 (pttp) REVERT: A 703 ASN cc_start: 0.8403 (t0) cc_final: 0.7955 (t0) REVERT: A 779 GLN cc_start: 0.8719 (tp40) cc_final: 0.8458 (tm-30) REVERT: A 900 MET cc_start: 0.8929 (mtp) cc_final: 0.8671 (mtm) REVERT: A 1092 GLU cc_start: 0.8471 (pt0) cc_final: 0.8093 (pm20) REVERT: B 88 ASP cc_start: 0.7989 (t0) cc_final: 0.7722 (t0) REVERT: C 153 MET cc_start: 0.8402 (mtp) cc_final: 0.8190 (mtp) REVERT: C 486 PHE cc_start: 0.8429 (t80) cc_final: 0.7684 (t80) REVERT: C 1019 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.7999 (tpt170) outliers start: 26 outliers final: 20 residues processed: 99 average time/residue: 0.6069 time to fit residues: 71.5167 Evaluate side-chains 102 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 36 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 191 optimal weight: 0.0270 chunk 176 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.066553 restraints weight = 62365.338| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.96 r_work: 0.3060 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27360 Z= 0.121 Angle : 0.526 9.561 37368 Z= 0.273 Chirality : 0.044 0.255 4363 Planarity : 0.004 0.060 4733 Dihedral : 4.908 56.415 4849 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 0.80 % Allowed : 8.71 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3273 helix: 2.29 (0.19), residues: 746 sheet: 0.35 (0.19), residues: 735 loop : -0.78 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 346 TYR 0.020 0.001 TYR B 265 PHE 0.031 0.001 PHE B 823 TRP 0.008 0.001 TRP A 152 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00276 (27250) covalent geometry : angle 0.51309 (37086) SS BOND : bond 0.00197 ( 48) SS BOND : angle 1.30442 ( 96) hydrogen bonds : bond 0.04378 ( 1117) hydrogen bonds : angle 5.37732 ( 3066) link_BETA1-4 : bond 0.00355 ( 14) link_BETA1-4 : angle 1.10059 ( 42) link_NAG-ASN : bond 0.00273 ( 48) link_NAG-ASN : angle 1.60520 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.73 seconds wall clock time: 97 minutes 55.93 seconds (5875.93 seconds total)