Starting phenix.real_space_refine on Thu Mar 5 13:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kea_22836/03_2026/7kea_22836.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 96 5.16 5 C 14236 2.51 5 N 3682 2.21 5 O 4337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 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: 22351 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 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 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: 5.38, per 1000 atoms: 0.24 Number of scatterers: 22351 At special positions: 0 Unit cell: (138.598, 129.076, 178.802, 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 96 16.00 O 4337 8.00 N 3682 7.00 C 14236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 984.7 milliseconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 42 sheets defined 28.3% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.988A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.798A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.356A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.593A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.518A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.521A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.989A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.756A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.150A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 4.016A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.688A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.590A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.868A pdb=" N ASN B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.558A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.535A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.479A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 889 removed outlier: 4.124A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.553A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.550A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.251A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.888A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.873A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.246A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.636A pdb=" N ASP C 420 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.473A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.627A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.464A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.956A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.985A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.832A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.683A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.624A 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 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.131A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 4.187A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.987A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.303A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.507A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.096A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.078A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.777A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.962A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.613A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.044A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.107A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.591A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.958A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.306A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.658A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.926A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.875A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.699A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.506A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.118A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.508A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.807A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.958A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 451 through 453 removed outlier: 4.508A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.692A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.652A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C1066 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.652A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C1066 " --> pdb=" O SER C 721 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 986 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4070 1.32 - 1.44: 5650 1.44 - 1.57: 12958 1.57 - 1.70: 1 1.70 - 1.83: 120 Bond restraints: 22799 Sorted by residual: bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 22794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 27939 3.02 - 6.05: 3063 6.05 - 9.07: 67 9.07 - 12.09: 3 12.09 - 15.12: 1 Bond angle restraints: 31073 Sorted by residual: angle pdb=" N LEU B 582 " pdb=" CA LEU B 582 " pdb=" C LEU B 582 " ideal model delta sigma weight residual 110.80 125.92 -15.12 2.13e+00 2.20e-01 5.04e+01 angle pdb=" CA ASP C 427 " pdb=" CB ASP C 427 " pdb=" CG ASP C 427 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.48e+01 angle pdb=" CA PHE C 377 " pdb=" CB PHE C 377 " pdb=" CG PHE C 377 " ideal model delta sigma weight residual 113.80 120.22 -6.42 1.00e+00 1.00e+00 4.12e+01 angle pdb=" CA PHE C 106 " pdb=" CB PHE C 106 " pdb=" CG PHE C 106 " ideal model delta sigma weight residual 113.80 120.21 -6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" CA PHE C 347 " pdb=" CB PHE C 347 " pdb=" CG PHE C 347 " ideal model delta sigma weight residual 113.80 120.10 -6.30 1.00e+00 1.00e+00 3.97e+01 ... (remaining 31068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 13383 19.96 - 39.91: 697 39.91 - 59.87: 118 59.87 - 79.83: 54 79.83 - 99.78: 21 Dihedral angle restraints: 14273 sinusoidal: 5932 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.83 -88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 -179.62 -87.38 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 178.42 -85.42 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 14270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2606 0.096 - 0.191: 1032 0.191 - 0.287: 166 0.287 - 0.382: 8 0.382 - 0.478: 5 Chirality restraints: 3817 Sorted by residual: 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 -2.58 0.18 2.00e-02 2.50e+03 8.19e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.08e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 ... (remaining 3814 not shown) Planarity restraints: 3974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.228 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 331 " -0.144 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.480 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.204 2.00e-02 2.50e+03 2.36e-01 6.95e+02 pdb=" CG ASN C1074 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.377 2.00e-02 2.50e+03 pdb=" C1 NAG C1311 " 0.284 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.181 2.00e-02 2.50e+03 2.02e-01 5.08e+02 pdb=" CG ASN B 603 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.316 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.242 2.00e-02 2.50e+03 ... (remaining 3971 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 1 1.86 - 2.62: 48 2.62 - 3.38: 28749 3.38 - 4.14: 54292 4.14 - 4.90: 96337 Nonbonded interactions: 179427 Sorted by model distance: nonbonded pdb=" O GLY B 339 " pdb=" OD1 ASN B 343 " model vdw 1.103 3.040 nonbonded pdb=" C GLY B 339 " pdb=" OD1 ASN B 343 " model vdw 2.210 3.270 nonbonded pdb=" O GLY B 339 " pdb=" CG ASN B 343 " model vdw 2.318 3.270 nonbonded pdb=" CB LEU A 118 " pdb=" CZ PHE A 133 " model vdw 2.390 3.740 nonbonded pdb=" OE1 GLN C 607 " pdb=" CE1 TYR C 674 " model vdw 2.407 3.340 ... (remaining 179422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and ( \ name N or name CA or name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.110 Find NCS groups from input model: 0.730 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.079 22892 Z= 0.778 Angle : 1.861 15.119 31317 Z= 1.218 Chirality : 0.096 0.478 3817 Planarity : 0.014 0.166 3928 Dihedral : 13.427 99.782 8770 Min Nonbonded Distance : 1.103 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.15 % Favored : 92.42 % Rotamer: Outliers : 1.24 % Allowed : 3.77 % Favored : 94.99 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 2797 helix: -1.28 (0.17), residues: 659 sheet: 0.04 (0.24), residues: 426 loop : -1.55 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 273 TYR 0.134 0.022 TYR A 279 PHE 0.093 0.015 PHE A 802 TRP 0.137 0.027 TRP A 886 HIS 0.014 0.004 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.01335 (22799) covalent geometry : angle 1.83503 (31073) SS BOND : bond 0.01268 ( 35) SS BOND : angle 1.99123 ( 70) hydrogen bonds : bond 0.16080 ( 976) hydrogen bonds : angle 9.06964 ( 2673) link_BETA1-4 : bond 0.02248 ( 12) link_BETA1-4 : angle 4.13473 ( 36) link_NAG-ASN : bond 0.01472 ( 46) link_NAG-ASN : angle 4.61887 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8204 (mtm110) REVERT: A 353 TRP cc_start: 0.7503 (p-90) cc_final: 0.6614 (p-90) REVERT: A 389 ASP cc_start: 0.8047 (m-30) cc_final: 0.7766 (t0) REVERT: A 464 PHE cc_start: 0.8675 (m-80) cc_final: 0.8236 (m-80) REVERT: A 508 TYR cc_start: 0.8478 (m-80) cc_final: 0.8164 (m-80) REVERT: A 697 MET cc_start: 0.8350 (ptm) cc_final: 0.8031 (ptm) REVERT: A 776 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8740 (ttmm) REVERT: A 965 GLN cc_start: 0.9064 (mm110) cc_final: 0.8863 (mm-40) REVERT: A 966 LEU cc_start: 0.9443 (mt) cc_final: 0.9155 (mp) REVERT: A 987 VAL cc_start: 0.8849 (t) cc_final: 0.8408 (m) REVERT: A 1004 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9201 (tt) REVERT: B 776 LYS cc_start: 0.9422 (tttt) cc_final: 0.8869 (ttpp) REVERT: B 964 LYS cc_start: 0.9262 (mttt) cc_final: 0.9050 (mttp) REVERT: B 976 VAL cc_start: 0.9362 (t) cc_final: 0.9017 (t) REVERT: B 979 ASP cc_start: 0.9221 (m-30) cc_final: 0.8999 (m-30) REVERT: B 1004 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9048 (tt) REVERT: B 1107 ARG cc_start: 0.7857 (ptp90) cc_final: 0.7396 (ptp-170) REVERT: B 1113 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7724 (mp10) REVERT: C 200 TYR cc_start: 0.8746 (m-80) cc_final: 0.8415 (m-80) REVERT: C 318 PHE cc_start: 0.8651 (t80) cc_final: 0.8263 (t80) REVERT: C 565 PHE cc_start: 0.8019 (p90) cc_final: 0.7621 (p90) REVERT: C 740 MET cc_start: 0.8866 (ttt) cc_final: 0.8642 (ttp) REVERT: C 976 VAL cc_start: 0.9032 (t) cc_final: 0.8582 (p) REVERT: C 979 ASP cc_start: 0.8921 (m-30) cc_final: 0.8612 (m-30) REVERT: C 1004 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9185 (tt) outliers start: 28 outliers final: 7 residues processed: 254 average time/residue: 0.1763 time to fit residues: 68.8438 Evaluate side-chains 119 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 211 ASN A 218 GLN A 394 ASN A 414 GLN A 460 ASN A 856 ASN A 969 ASN A1088 HIS B 580 GLN B 907 ASN B1088 HIS C 493 GLN C 762 GLN C1005 GLN C1010 GLN C1088 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.087524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060455 restraints weight = 66233.627| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.75 r_work: 0.3057 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22892 Z= 0.159 Angle : 0.731 14.359 31317 Z= 0.369 Chirality : 0.047 0.347 3817 Planarity : 0.004 0.038 3928 Dihedral : 7.309 82.031 4262 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.51 % Allowed : 7.27 % Favored : 91.23 % 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: -0.80 (0.15), residues: 2797 helix: 0.31 (0.19), residues: 676 sheet: -0.16 (0.20), residues: 577 loop : -1.04 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 408 TYR 0.036 0.002 TYR A 421 PHE 0.027 0.002 PHE C 194 TRP 0.026 0.002 TRP A 104 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00343 (22799) covalent geometry : angle 0.67381 (31073) SS BOND : bond 0.00395 ( 35) SS BOND : angle 1.92141 ( 70) hydrogen bonds : bond 0.04846 ( 976) hydrogen bonds : angle 6.65413 ( 2673) link_BETA1-4 : bond 0.00261 ( 12) link_BETA1-4 : angle 1.66837 ( 36) link_NAG-ASN : bond 0.00497 ( 46) link_NAG-ASN : angle 4.04777 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8281 (mtm110) REVERT: A 389 ASP cc_start: 0.8432 (m-30) cc_final: 0.8142 (t0) REVERT: A 424 LYS cc_start: 0.8283 (tttt) cc_final: 0.7923 (pttp) REVERT: A 869 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8497 (ttm) REVERT: A 965 GLN cc_start: 0.9205 (mm110) cc_final: 0.8920 (mm-40) REVERT: A 1004 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9161 (tt) REVERT: A 1029 MET cc_start: 0.8352 (ttm) cc_final: 0.8143 (ttm) REVERT: B 740 MET cc_start: 0.8954 (tpt) cc_final: 0.8580 (tpt) REVERT: B 964 LYS cc_start: 0.9329 (mttt) cc_final: 0.9073 (mtmm) REVERT: B 979 ASP cc_start: 0.9264 (m-30) cc_final: 0.8663 (t70) REVERT: B 1004 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9064 (tt) REVERT: B 1113 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7693 (mp10) REVERT: C 200 TYR cc_start: 0.8741 (m-80) cc_final: 0.8438 (m-80) REVERT: C 318 PHE cc_start: 0.8852 (t80) cc_final: 0.8347 (t80) REVERT: C 392 PHE cc_start: 0.7920 (m-80) cc_final: 0.7649 (m-80) REVERT: C 571 ASP cc_start: 0.8298 (t0) cc_final: 0.7943 (t0) outliers start: 34 outliers final: 15 residues processed: 151 average time/residue: 0.1642 time to fit residues: 39.0577 Evaluate side-chains 105 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 10 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 chunk 225 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 127 optimal weight: 0.0970 chunk 122 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 394 ASN A 762 GLN A 856 ASN B 66 HIS B 901 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 901 GLN C1058 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.085715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058661 restraints weight = 67016.130| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.74 r_work: 0.3013 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22892 Z= 0.199 Angle : 0.658 11.478 31317 Z= 0.332 Chirality : 0.045 0.274 3817 Planarity : 0.004 0.041 3928 Dihedral : 6.382 67.707 4248 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.73 % Allowed : 8.46 % Favored : 89.81 % 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 (0.15), residues: 2797 helix: 0.71 (0.20), residues: 670 sheet: -0.28 (0.20), residues: 626 loop : -0.90 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.025 0.002 TYR C1067 PHE 0.026 0.002 PHE A 238 TRP 0.016 0.002 TRP A 104 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00450 (22799) covalent geometry : angle 0.62164 (31073) SS BOND : bond 0.00309 ( 35) SS BOND : angle 1.44861 ( 70) hydrogen bonds : bond 0.04394 ( 976) hydrogen bonds : angle 6.22194 ( 2673) link_BETA1-4 : bond 0.00169 ( 12) link_BETA1-4 : angle 1.40228 ( 36) link_NAG-ASN : bond 0.00335 ( 46) link_NAG-ASN : angle 3.13055 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.9006 (mtt90) cc_final: 0.8392 (mtm110) REVERT: A 869 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: B 740 MET cc_start: 0.8925 (tpt) cc_final: 0.8550 (tpt) REVERT: B 1004 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9076 (tt) REVERT: B 1050 MET cc_start: 0.7962 (ptm) cc_final: 0.7709 (ptt) REVERT: B 1113 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7565 (mt0) REVERT: C 200 TYR cc_start: 0.8741 (m-80) cc_final: 0.8428 (m-80) REVERT: C 318 PHE cc_start: 0.8950 (t80) cc_final: 0.8471 (t80) REVERT: C 427 ASP cc_start: 0.7736 (m-30) cc_final: 0.7510 (p0) REVERT: C 565 PHE cc_start: 0.8209 (p90) cc_final: 0.7261 (p90) REVERT: C 571 ASP cc_start: 0.8219 (t0) cc_final: 0.7800 (t0) REVERT: C 979 ASP cc_start: 0.9390 (m-30) cc_final: 0.9102 (m-30) outliers start: 39 outliers final: 23 residues processed: 131 average time/residue: 0.1570 time to fit residues: 32.7952 Evaluate side-chains 103 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 245 optimal weight: 0.0980 chunk 154 optimal weight: 0.8980 chunk 205 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 195 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN B 901 GLN B 913 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.086876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059892 restraints weight = 66159.992| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.74 r_work: 0.3048 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22892 Z= 0.119 Angle : 0.584 10.750 31317 Z= 0.294 Chirality : 0.044 0.253 3817 Planarity : 0.004 0.052 3928 Dihedral : 5.704 48.072 4246 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.77 % Allowed : 8.91 % Favored : 89.32 % 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: -0.29 (0.16), residues: 2797 helix: 1.18 (0.20), residues: 651 sheet: -0.34 (0.20), residues: 603 loop : -0.70 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE A 238 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00259 (22799) covalent geometry : angle 0.54771 (31073) SS BOND : bond 0.00264 ( 35) SS BOND : angle 1.64843 ( 70) hydrogen bonds : bond 0.03950 ( 976) hydrogen bonds : angle 5.95778 ( 2673) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.22484 ( 36) link_NAG-ASN : bond 0.00332 ( 46) link_NAG-ASN : angle 2.84954 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8379 (mtm110) REVERT: A 762 GLN cc_start: 0.9008 (pt0) cc_final: 0.8739 (pt0) REVERT: A 869 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8545 (ttm) REVERT: A 1004 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 740 MET cc_start: 0.8879 (tpt) cc_final: 0.8311 (tpt) REVERT: B 1004 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9068 (tt) REVERT: B 1113 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7337 (mt0) REVERT: C 200 TYR cc_start: 0.8674 (m-80) cc_final: 0.8406 (m-80) REVERT: C 318 PHE cc_start: 0.8942 (t80) cc_final: 0.8412 (t80) REVERT: C 565 PHE cc_start: 0.8127 (p90) cc_final: 0.7078 (p90) REVERT: C 571 ASP cc_start: 0.8283 (t0) cc_final: 0.7968 (t0) outliers start: 40 outliers final: 22 residues processed: 135 average time/residue: 0.1626 time to fit residues: 35.0270 Evaluate side-chains 102 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 85 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 228 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 283 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058839 restraints weight = 64824.078| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.67 r_work: 0.3001 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22892 Z= 0.170 Angle : 0.598 13.882 31317 Z= 0.298 Chirality : 0.044 0.279 3817 Planarity : 0.004 0.050 3928 Dihedral : 5.297 59.765 4246 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 9.92 % Favored : 88.17 % 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: -0.28 (0.16), residues: 2797 helix: 1.18 (0.20), residues: 660 sheet: -0.36 (0.20), residues: 637 loop : -0.69 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.022 0.001 TYR C1067 PHE 0.019 0.001 PHE A 238 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00382 (22799) covalent geometry : angle 0.56152 (31073) SS BOND : bond 0.00292 ( 35) SS BOND : angle 1.84370 ( 70) hydrogen bonds : bond 0.03974 ( 976) hydrogen bonds : angle 5.87704 ( 2673) link_BETA1-4 : bond 0.00195 ( 12) link_BETA1-4 : angle 1.20200 ( 36) link_NAG-ASN : bond 0.00332 ( 46) link_NAG-ASN : angle 2.83369 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.9012 (mtt90) cc_final: 0.8506 (mtm110) REVERT: A 408 ARG cc_start: 0.8929 (tmm160) cc_final: 0.8685 (ttp80) REVERT: A 508 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 740 MET cc_start: 0.9104 (mmm) cc_final: 0.8861 (mmm) REVERT: A 762 GLN cc_start: 0.9003 (pt0) cc_final: 0.8723 (pt0) REVERT: A 858 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8732 (pt) REVERT: A 869 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (ttm) REVERT: A 1004 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9145 (tt) REVERT: B 1004 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9137 (tt) REVERT: B 1107 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.8054 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7317 (mt0) REVERT: C 200 TYR cc_start: 0.8627 (m-80) cc_final: 0.8365 (m-80) REVERT: C 318 PHE cc_start: 0.8987 (t80) cc_final: 0.8405 (t80) REVERT: C 565 PHE cc_start: 0.8146 (p90) cc_final: 0.7079 (p90) REVERT: C 571 ASP cc_start: 0.8280 (t0) cc_final: 0.7952 (t0) outliers start: 43 outliers final: 27 residues processed: 122 average time/residue: 0.1600 time to fit residues: 31.6224 Evaluate side-chains 104 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 255 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 132 optimal weight: 0.0040 chunk 209 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 872 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059541 restraints weight = 65072.147| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.69 r_work: 0.3019 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 22892 Z= 0.135 Angle : 0.554 13.140 31317 Z= 0.278 Chirality : 0.043 0.229 3817 Planarity : 0.004 0.048 3928 Dihedral : 4.947 55.820 4246 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.95 % Allowed : 10.32 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2797 helix: 1.28 (0.20), residues: 668 sheet: -0.37 (0.20), residues: 634 loop : -0.63 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.020 0.001 TYR C1067 PHE 0.017 0.001 PHE C 374 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00302 (22799) covalent geometry : angle 0.52083 (31073) SS BOND : bond 0.00322 ( 35) SS BOND : angle 1.73870 ( 70) hydrogen bonds : bond 0.03749 ( 976) hydrogen bonds : angle 5.72351 ( 2673) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.11350 ( 36) link_NAG-ASN : bond 0.00352 ( 46) link_NAG-ASN : angle 2.60117 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8502 (t0) cc_final: 0.8220 (t0) REVERT: A 508 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 762 GLN cc_start: 0.8958 (pt0) cc_final: 0.8729 (pt0) REVERT: A 858 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8685 (pt) REVERT: A 869 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8619 (ttm) REVERT: A 1004 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9124 (tt) REVERT: B 533 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9066 (mt) REVERT: B 902 MET cc_start: 0.8567 (tpp) cc_final: 0.8313 (tpp) REVERT: B 1050 MET cc_start: 0.8283 (ptp) cc_final: 0.8045 (ptt) REVERT: B 1107 ARG cc_start: 0.8407 (ptp-170) cc_final: 0.8069 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7344 (mt0) REVERT: C 200 TYR cc_start: 0.8583 (m-80) cc_final: 0.8357 (m-80) REVERT: C 318 PHE cc_start: 0.8977 (t80) cc_final: 0.8403 (t80) REVERT: C 565 PHE cc_start: 0.8129 (p90) cc_final: 0.7033 (p90) REVERT: C 571 ASP cc_start: 0.8217 (t0) cc_final: 0.7914 (t0) outliers start: 44 outliers final: 23 residues processed: 126 average time/residue: 0.1347 time to fit residues: 28.1271 Evaluate side-chains 105 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.0060 chunk 229 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 31 optimal weight: 0.0470 chunk 226 optimal weight: 30.0000 chunk 159 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.7696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060019 restraints weight = 66188.720| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.80 r_work: 0.3029 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 22892 Z= 0.110 Angle : 0.540 12.931 31317 Z= 0.270 Chirality : 0.043 0.209 3817 Planarity : 0.003 0.050 3928 Dihedral : 4.653 50.100 4244 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.60 % Allowed : 10.99 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2797 helix: 1.38 (0.20), residues: 669 sheet: -0.29 (0.20), residues: 649 loop : -0.60 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE A 456 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00241 (22799) covalent geometry : angle 0.50851 (31073) SS BOND : bond 0.00248 ( 35) SS BOND : angle 1.68984 ( 70) hydrogen bonds : bond 0.03615 ( 976) hydrogen bonds : angle 5.57008 ( 2673) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 1.03597 ( 36) link_NAG-ASN : bond 0.00361 ( 46) link_NAG-ASN : angle 2.49539 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8440 (t0) cc_final: 0.8154 (t0) REVERT: A 408 ARG cc_start: 0.8966 (tmm160) cc_final: 0.8674 (ttp80) REVERT: A 508 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8302 (t80) REVERT: A 1004 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9139 (tt) REVERT: B 226 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 1050 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7837 (ptm) REVERT: B 1107 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.8089 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7360 (mt0) REVERT: C 200 TYR cc_start: 0.8550 (m-80) cc_final: 0.8343 (m-80) REVERT: C 318 PHE cc_start: 0.8961 (t80) cc_final: 0.8410 (t80) REVERT: C 565 PHE cc_start: 0.8121 (p90) cc_final: 0.6997 (p90) REVERT: C 571 ASP cc_start: 0.8178 (t0) cc_final: 0.7863 (t0) outliers start: 36 outliers final: 22 residues processed: 115 average time/residue: 0.1318 time to fit residues: 25.6559 Evaluate side-chains 101 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 901 GLN B1088 HIS C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.085235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058261 restraints weight = 66047.675| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.77 r_work: 0.2993 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22892 Z= 0.179 Angle : 0.572 12.709 31317 Z= 0.285 Chirality : 0.043 0.200 3817 Planarity : 0.004 0.051 3928 Dihedral : 4.650 43.593 4244 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.95 % Allowed : 10.63 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2797 helix: 1.34 (0.20), residues: 669 sheet: -0.28 (0.20), residues: 658 loop : -0.58 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.021 0.001 TYR C1067 PHE 0.026 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00403 (22799) covalent geometry : angle 0.54297 (31073) SS BOND : bond 0.00287 ( 35) SS BOND : angle 1.63349 ( 70) hydrogen bonds : bond 0.03774 ( 976) hydrogen bonds : angle 5.67283 ( 2673) link_BETA1-4 : bond 0.00228 ( 12) link_BETA1-4 : angle 1.10962 ( 36) link_NAG-ASN : bond 0.00336 ( 46) link_NAG-ASN : angle 2.50421 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 76 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8482 (t0) cc_final: 0.8179 (t0) REVERT: A 508 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 226 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 533 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9033 (mt) REVERT: B 1107 ARG cc_start: 0.8358 (ptp-170) cc_final: 0.8011 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7402 (mt0) REVERT: C 318 PHE cc_start: 0.8998 (t80) cc_final: 0.8471 (t80) REVERT: C 565 PHE cc_start: 0.8155 (p90) cc_final: 0.7089 (p90) REVERT: C 571 ASP cc_start: 0.8126 (t0) cc_final: 0.7856 (t0) outliers start: 44 outliers final: 26 residues processed: 115 average time/residue: 0.1377 time to fit residues: 26.7918 Evaluate side-chains 102 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 57 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN B 901 GLN C 901 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.086321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059472 restraints weight = 66404.799| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.80 r_work: 0.3023 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22892 Z= 0.119 Angle : 0.535 12.427 31317 Z= 0.266 Chirality : 0.042 0.202 3817 Planarity : 0.003 0.051 3928 Dihedral : 4.466 44.325 4244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.42 % Allowed : 11.25 % Favored : 87.33 % 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: -0.03 (0.16), residues: 2797 helix: 1.43 (0.20), residues: 671 sheet: -0.30 (0.20), residues: 609 loop : -0.52 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.019 0.001 TYR C1067 PHE 0.026 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (22799) covalent geometry : angle 0.50730 (31073) SS BOND : bond 0.00214 ( 35) SS BOND : angle 1.40797 ( 70) hydrogen bonds : bond 0.03540 ( 976) hydrogen bonds : angle 5.51316 ( 2673) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 0.98445 ( 36) link_NAG-ASN : bond 0.00357 ( 46) link_NAG-ASN : angle 2.38974 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8437 (t0) cc_final: 0.8135 (t0) REVERT: A 508 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 226 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 1107 ARG cc_start: 0.8377 (ptp-170) cc_final: 0.8076 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7411 (mt0) REVERT: C 318 PHE cc_start: 0.8939 (t80) cc_final: 0.8434 (t80) REVERT: C 565 PHE cc_start: 0.8126 (p90) cc_final: 0.7034 (p90) REVERT: C 571 ASP cc_start: 0.8089 (t0) cc_final: 0.7776 (t0) outliers start: 32 outliers final: 25 residues processed: 108 average time/residue: 0.1390 time to fit residues: 25.1674 Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 196 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN B 901 GLN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057692 restraints weight = 66612.860| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.77 r_work: 0.2979 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22892 Z= 0.209 Angle : 0.592 12.379 31317 Z= 0.297 Chirality : 0.044 0.208 3817 Planarity : 0.004 0.052 3928 Dihedral : 4.601 43.377 4244 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.64 % Allowed : 11.08 % Favored : 87.28 % 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: -0.13 (0.16), residues: 2797 helix: 1.34 (0.20), residues: 669 sheet: -0.32 (0.20), residues: 659 loop : -0.59 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.024 0.002 TYR C1067 PHE 0.025 0.002 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00472 (22799) covalent geometry : angle 0.56580 (31073) SS BOND : bond 0.00323 ( 35) SS BOND : angle 1.53978 ( 70) hydrogen bonds : bond 0.03849 ( 976) hydrogen bonds : angle 5.70902 ( 2673) link_BETA1-4 : bond 0.00208 ( 12) link_BETA1-4 : angle 1.10796 ( 36) link_NAG-ASN : bond 0.00349 ( 46) link_NAG-ASN : angle 2.45044 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8406 (t0) cc_final: 0.8100 (t0) REVERT: A 508 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8287 (t80) REVERT: B 226 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 533 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9032 (mt) REVERT: B 1107 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.7985 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7392 (mt0) REVERT: C 318 PHE cc_start: 0.8992 (t80) cc_final: 0.8484 (t80) REVERT: C 565 PHE cc_start: 0.8157 (p90) cc_final: 0.7126 (p90) REVERT: C 571 ASP cc_start: 0.8107 (t0) cc_final: 0.7836 (t0) outliers start: 37 outliers final: 29 residues processed: 104 average time/residue: 0.1396 time to fit residues: 24.4813 Evaluate side-chains 104 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 265 optimal weight: 0.0040 chunk 149 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN B 901 GLN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.086166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059310 restraints weight = 65984.152| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.80 r_work: 0.3019 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22892 Z= 0.117 Angle : 0.538 12.276 31317 Z= 0.268 Chirality : 0.043 0.201 3817 Planarity : 0.003 0.052 3928 Dihedral : 4.436 42.454 4244 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.24 % Allowed : 11.48 % Favored : 87.28 % 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: -0.05 (0.16), residues: 2797 helix: 1.43 (0.20), residues: 669 sheet: -0.36 (0.20), residues: 627 loop : -0.50 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE C 168 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (22799) covalent geometry : angle 0.51172 (31073) SS BOND : bond 0.00220 ( 35) SS BOND : angle 1.34091 ( 70) hydrogen bonds : bond 0.03558 ( 976) hydrogen bonds : angle 5.52895 ( 2673) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 0.97415 ( 36) link_NAG-ASN : bond 0.00358 ( 46) link_NAG-ASN : angle 2.34958 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.25 seconds wall clock time: 100 minutes 18.94 seconds (6018.94 seconds total)