Starting phenix.real_space_refine on Fri Sep 19 11:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eli_48150/09_2025/9eli_48150.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 111 5.16 5 C 16275 2.51 5 N 4146 2.21 5 O 4977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25509 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "B" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "C" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.40, per 1000 atoms: 0.29 Number of scatterers: 25509 At special positions: 0 Unit cell: (135.702, 135.702, 185.962, 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 111 16.00 O 4977 8.00 N 4146 7.00 C 16275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.36 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=1.36 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=1.36 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 354 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 354 " " NAG B1305 " - " ASN B 343 " " NAG B1307 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 354 " " NAG C1305 " - " ASN C 343 " " NAG C1307 " - " ASN C 30 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 282 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " NAG-THR " NAG A1306 " - " THR A 236 " " NAG B1306 " - " THR B 236 " " NAG C1306 " - " THR C 236 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5910 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 39 sheets defined 26.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.555A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.101A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (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 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.671A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.856A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.100A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.671A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1150 removed outlier: 3.856A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.555A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.100A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.671A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1150 removed outlier: 3.857A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE A 32 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 60 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.057A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 172 removed outlier: 7.055A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.973A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.391A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.383A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.070A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE B 32 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER B 60 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.056A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 163 through 172 removed outlier: 7.054A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.972A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.392A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AC3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.384A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.366A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.070A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE C 32 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 60 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.057A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 163 through 172 removed outlier: 7.055A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.973A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.392A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.383A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.53: 24289 1.53 - 1.85: 1805 1.85 - 2.17: 0 2.17 - 2.49: 0 2.49 - 2.81: 3 Bond restraints: 26097 Sorted by residual: bond pdb=" C LYS C 679 " pdb=" N SER C 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C LYS B 679 " pdb=" N SER B 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C LYS A 679 " pdb=" N SER A 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 26092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.98: 35484 11.98 - 23.96: 9 23.96 - 35.94: 3 35.94 - 47.92: 0 47.92 - 59.90: 3 Bond angle restraints: 35499 Sorted by residual: angle pdb=" O LYS C 679 " pdb=" C LYS C 679 " pdb=" N SER C 689 " ideal model delta sigma weight residual 122.59 62.69 59.90 1.33e+00 5.65e-01 2.03e+03 angle pdb=" O LYS B 679 " pdb=" C LYS B 679 " pdb=" N SER B 689 " ideal model delta sigma weight residual 122.59 62.72 59.87 1.33e+00 5.65e-01 2.03e+03 angle pdb=" O LYS A 679 " pdb=" C LYS A 679 " pdb=" N SER A 689 " ideal model delta sigma weight residual 122.59 62.72 59.87 1.33e+00 5.65e-01 2.03e+03 angle pdb=" C LYS C 679 " pdb=" N SER C 689 " pdb=" CA SER C 689 " ideal model delta sigma weight residual 121.54 148.49 -26.95 1.91e+00 2.74e-01 1.99e+02 angle pdb=" C LYS A 679 " pdb=" N SER A 689 " pdb=" CA SER A 689 " ideal model delta sigma weight residual 121.54 148.48 -26.94 1.91e+00 2.74e-01 1.99e+02 ... (remaining 35494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14950 17.92 - 35.84: 1007 35.84 - 53.76: 246 53.76 - 71.68: 51 71.68 - 89.60: 39 Dihedral angle restraints: 16293 sinusoidal: 7110 harmonic: 9183 Sorted by residual: dihedral pdb=" CA ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta harmonic sigma weight residual 180.00 146.94 33.06 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual 180.00 147.00 33.00 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 16290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3024 0.053 - 0.106: 849 0.106 - 0.158: 264 0.158 - 0.211: 27 0.211 - 0.264: 15 Chirality restraints: 4179 Sorted by residual: chirality pdb=" CG LEU A 878 " pdb=" CB LEU A 878 " pdb=" CD1 LEU A 878 " pdb=" CD2 LEU A 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B 878 " pdb=" CB LEU B 878 " pdb=" CD1 LEU B 878 " pdb=" CD2 LEU B 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU C 878 " pdb=" CB LEU C 878 " pdb=" CD1 LEU C 878 " pdb=" CD2 LEU C 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4176 not shown) Planarity restraints: 4533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 679 " 0.189 2.00e-02 2.50e+03 2.84e-01 8.05e+02 pdb=" C LYS B 679 " -0.449 2.00e-02 2.50e+03 pdb=" O LYS B 679 " 0.289 2.00e-02 2.50e+03 pdb=" N SER B 689 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 679 " -0.189 2.00e-02 2.50e+03 2.84e-01 8.05e+02 pdb=" C LYS C 679 " 0.449 2.00e-02 2.50e+03 pdb=" O LYS C 679 " -0.289 2.00e-02 2.50e+03 pdb=" N SER C 689 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 679 " -0.189 2.00e-02 2.50e+03 2.84e-01 8.04e+02 pdb=" C LYS A 679 " 0.449 2.00e-02 2.50e+03 pdb=" O LYS A 679 " -0.289 2.00e-02 2.50e+03 pdb=" N SER A 689 " 0.029 2.00e-02 2.50e+03 ... (remaining 4530 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 168 2.63 - 3.20: 22573 3.20 - 3.77: 38022 3.77 - 4.33: 54740 4.33 - 4.90: 90477 Nonbonded interactions: 205980 Sorted by model distance: nonbonded pdb=" O ASN C 331 " pdb=" OD1 ASN C 331 " model vdw 2.066 3.040 nonbonded pdb=" O ASN B 331 " pdb=" OD1 ASN B 331 " model vdw 2.068 3.040 nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 331 " model vdw 2.068 3.040 nonbonded pdb=" O CYS C 851 " pdb=" CD2 PHE C 855 " model vdw 2.222 3.340 nonbonded pdb=" O CYS A 851 " pdb=" CD2 PHE A 855 " model vdw 2.223 3.340 ... (remaining 205975 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.520 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.019 1.476 26190 Z= 1.223 Angle : 1.303 59.903 35739 Z= 0.737 Chirality : 0.056 0.264 4179 Planarity : 0.011 0.284 4500 Dihedral : 13.854 89.603 10275 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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 aren not related in a simple way. whole: 0.03 (0.14), residues: 3105 helix: 2.01 (0.20), residues: 693 sheet: -0.17 (0.20), residues: 561 loop : -0.69 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG A 567 TYR 0.031 0.002 TYR C 200 PHE 0.053 0.003 PHE A 92 TRP 0.023 0.002 TRP A 436 HIS 0.003 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.01724 (26097) covalent geometry : angle 1.19361 (35499) SS BOND : bond 0.19363 ( 36) SS BOND : angle 10.81232 ( 72) hydrogen bonds : bond 0.12499 ( 1008) hydrogen bonds : angle 6.94393 ( 2826) link_BETA1-4 : bond 0.00663 ( 21) link_BETA1-4 : angle 3.51278 ( 63) link_NAG-ASN : bond 0.00206 ( 33) link_NAG-ASN : angle 2.86143 ( 99) link_NAG-THR : bond 0.00598 ( 3) link_NAG-THR : angle 4.36338 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.6906 (Cg_endo) cc_final: 0.6068 (Cg_endo) REVERT: A 177 MET cc_start: 0.2420 (ptp) cc_final: 0.1901 (pp-130) REVERT: A 205 SER cc_start: 0.8905 (p) cc_final: 0.8437 (t) REVERT: B 85 PRO cc_start: 0.6964 (Cg_endo) cc_final: 0.5994 (Cg_endo) REVERT: B 177 MET cc_start: 0.2603 (ptp) cc_final: 0.1767 (pp-130) REVERT: B 205 SER cc_start: 0.8939 (p) cc_final: 0.8447 (t) REVERT: B 237 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7200 (ttp-110) REVERT: B 321 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 869 MET cc_start: 0.9150 (mtt) cc_final: 0.8882 (mtt) REVERT: C 177 MET cc_start: 0.2519 (ptp) cc_final: 0.1853 (pp-130) REVERT: C 205 SER cc_start: 0.8918 (p) cc_final: 0.8458 (t) REVERT: C 321 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8352 (mm-40) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.5337 time to fit residues: 152.7586 Evaluate side-chains 199 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 751 ASN A 804 GLN A 935 GLN B 613 GLN B 751 ASN B 804 GLN B 935 GLN C 613 GLN C 751 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.201022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161916 restraints weight = 27625.877| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.57 r_work: 0.3316 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26190 Z= 0.209 Angle : 0.692 11.081 35739 Z= 0.345 Chirality : 0.049 0.317 4179 Planarity : 0.005 0.037 4500 Dihedral : 6.284 45.214 4557 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.77 % Allowed : 9.20 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3111 helix: 1.91 (0.19), residues: 732 sheet: 0.11 (0.20), residues: 591 loop : -0.76 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.023 0.002 TYR A 170 PHE 0.025 0.002 PHE A 855 TRP 0.012 0.002 TRP C 633 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00496 (26097) covalent geometry : angle 0.66305 (35499) SS BOND : bond 0.00546 ( 36) SS BOND : angle 1.10291 ( 72) hydrogen bonds : bond 0.05229 ( 1008) hydrogen bonds : angle 5.58669 ( 2826) link_BETA1-4 : bond 0.00647 ( 21) link_BETA1-4 : angle 3.33891 ( 63) link_NAG-ASN : bond 0.00494 ( 33) link_NAG-ASN : angle 2.63458 ( 99) link_NAG-THR : bond 0.00263 ( 3) link_NAG-THR : angle 2.10718 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6971 (mt) REVERT: A 205 SER cc_start: 0.8893 (p) cc_final: 0.8630 (t) REVERT: B 205 SER cc_start: 0.8877 (p) cc_final: 0.8605 (t) REVERT: C 205 SER cc_start: 0.8903 (p) cc_final: 0.8662 (t) REVERT: C 314 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7968 (tt0) outliers start: 49 outliers final: 20 residues processed: 243 average time/residue: 0.4773 time to fit residues: 141.3952 Evaluate side-chains 205 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 170 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 274 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 313 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 314 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 762 GLN A1119 ASN B 207 HIS B 613 GLN C 207 HIS C 321 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.202337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161121 restraints weight = 27666.116| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.72 r_work: 0.3321 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26190 Z= 0.124 Angle : 0.601 9.686 35739 Z= 0.299 Chirality : 0.044 0.202 4179 Planarity : 0.004 0.043 4500 Dihedral : 5.769 41.854 4557 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.73 % Allowed : 9.74 % Favored : 88.53 % 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 aren not related in a simple way. whole: 0.25 (0.14), residues: 3111 helix: 2.04 (0.19), residues: 735 sheet: 0.51 (0.20), residues: 609 loop : -0.79 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.020 0.001 TYR C 170 PHE 0.014 0.001 PHE C 371 TRP 0.010 0.001 TRP B 633 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00281 (26097) covalent geometry : angle 0.57056 (35499) SS BOND : bond 0.00232 ( 36) SS BOND : angle 1.50848 ( 72) hydrogen bonds : bond 0.04397 ( 1008) hydrogen bonds : angle 5.27523 ( 2826) link_BETA1-4 : bond 0.00486 ( 21) link_BETA1-4 : angle 3.04096 ( 63) link_NAG-ASN : bond 0.00360 ( 33) link_NAG-ASN : angle 2.42231 ( 99) link_NAG-THR : bond 0.00351 ( 3) link_NAG-THR : angle 1.95978 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8797 (p) cc_final: 0.8591 (t) REVERT: A 304 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7284 (mptp) REVERT: A 603 ASN cc_start: 0.7873 (p0) cc_final: 0.7477 (m110) REVERT: A 646 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7592 (mtp-110) REVERT: B 205 SER cc_start: 0.8818 (p) cc_final: 0.8614 (t) REVERT: B 269 TYR cc_start: 0.8477 (m-80) cc_final: 0.8108 (m-80) REVERT: B 304 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7387 (mptp) REVERT: C 304 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7756 (mptp) outliers start: 48 outliers final: 22 residues processed: 234 average time/residue: 0.4445 time to fit residues: 128.6250 Evaluate side-chains 199 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 162 optimal weight: 0.0870 chunk 246 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 241 optimal weight: 0.3980 chunk 177 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 280 ASN B 544 ASN B 613 GLN B 751 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 751 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158289 restraints weight = 27544.454| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.68 r_work: 0.3339 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26190 Z= 0.227 Angle : 0.665 10.601 35739 Z= 0.332 Chirality : 0.047 0.217 4179 Planarity : 0.005 0.048 4500 Dihedral : 5.930 40.494 4557 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.67 % Allowed : 10.25 % Favored : 87.09 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3111 helix: 1.88 (0.18), residues: 732 sheet: 0.27 (0.20), residues: 597 loop : -0.86 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.021 0.002 TYR A1067 PHE 0.018 0.002 PHE C 541 TRP 0.011 0.002 TRP A 633 HIS 0.008 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00551 (26097) covalent geometry : angle 0.63252 (35499) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.82450 ( 72) hydrogen bonds : bond 0.05250 ( 1008) hydrogen bonds : angle 5.40425 ( 2826) link_BETA1-4 : bond 0.00427 ( 21) link_BETA1-4 : angle 3.11715 ( 63) link_NAG-ASN : bond 0.00561 ( 33) link_NAG-ASN : angle 2.68844 ( 99) link_NAG-THR : bond 0.00629 ( 3) link_NAG-THR : angle 2.28370 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5054 (OUTLIER) cc_final: 0.4495 (p) REVERT: A 108 THR cc_start: 0.5429 (p) cc_final: 0.4962 (t) REVERT: A 304 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7414 (mptp) REVERT: A 314 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 646 ARG cc_start: 0.8599 (mtp85) cc_final: 0.7910 (mtp-110) REVERT: A 675 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.5944 (mp10) REVERT: B 108 THR cc_start: 0.5677 (p) cc_final: 0.5236 (t) REVERT: B 269 TYR cc_start: 0.8480 (m-80) cc_final: 0.8160 (m-80) REVERT: B 321 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8531 (mm-40) REVERT: B 675 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.5916 (mp10) REVERT: C 108 THR cc_start: 0.5492 (p) cc_final: 0.5153 (t) REVERT: C 314 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 675 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6026 (mp10) outliers start: 74 outliers final: 36 residues processed: 252 average time/residue: 0.4776 time to fit residues: 147.2931 Evaluate side-chains 222 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 205 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 251 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1119 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN B 564 GLN B1119 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 321 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.200149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164764 restraints weight = 27648.046| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.45 r_work: 0.3524 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26190 Z= 0.163 Angle : 0.603 9.748 35739 Z= 0.302 Chirality : 0.045 0.211 4179 Planarity : 0.004 0.045 4500 Dihedral : 5.670 39.795 4557 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.49 % Allowed : 10.89 % Favored : 86.62 % 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 aren not related in a simple way. whole: 0.10 (0.14), residues: 3111 helix: 1.90 (0.18), residues: 738 sheet: 0.40 (0.20), residues: 627 loop : -0.89 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.016 0.001 TYR A1067 PHE 0.015 0.001 PHE A 898 TRP 0.010 0.001 TRP C 633 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00388 (26097) covalent geometry : angle 0.57360 (35499) SS BOND : bond 0.00292 ( 36) SS BOND : angle 1.52384 ( 72) hydrogen bonds : bond 0.04580 ( 1008) hydrogen bonds : angle 5.20112 ( 2826) link_BETA1-4 : bond 0.00422 ( 21) link_BETA1-4 : angle 2.86380 ( 63) link_NAG-ASN : bond 0.00427 ( 33) link_NAG-ASN : angle 2.47980 ( 99) link_NAG-THR : bond 0.00509 ( 3) link_NAG-THR : angle 1.94060 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1805 (tpt) cc_final: -0.0524 (mpm) REVERT: A 190 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6835 (mtm110) REVERT: A 304 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7395 (mptp) REVERT: A 646 ARG cc_start: 0.8481 (mtp85) cc_final: 0.7939 (mtp-110) REVERT: A 675 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: B 675 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6123 (mp10) REVERT: B 790 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8460 (mttt) REVERT: C 153 MET cc_start: 0.1950 (OUTLIER) cc_final: 0.0093 (mpt) REVERT: C 281 GLU cc_start: 0.7794 (mp0) cc_final: 0.7577 (mp0) REVERT: C 675 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6142 (mp10) outliers start: 69 outliers final: 34 residues processed: 234 average time/residue: 0.4503 time to fit residues: 129.9944 Evaluate side-chains 211 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 169 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 280 ASN A 955 ASN A1119 ASN B 207 HIS B 280 ASN B1119 ASN C 207 HIS C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.201671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161679 restraints weight = 27727.508| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.69 r_work: 0.3504 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26190 Z= 0.122 Angle : 0.566 9.156 35739 Z= 0.282 Chirality : 0.044 0.208 4179 Planarity : 0.004 0.042 4500 Dihedral : 5.350 38.990 4557 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 11.47 % Favored : 86.22 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3111 helix: 2.08 (0.19), residues: 735 sheet: 0.40 (0.20), residues: 642 loop : -0.84 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.016 0.001 TYR B 660 PHE 0.015 0.001 PHE B 371 TRP 0.011 0.001 TRP A 633 HIS 0.003 0.000 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00279 (26097) covalent geometry : angle 0.53797 (35499) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.38216 ( 72) hydrogen bonds : bond 0.04138 ( 1008) hydrogen bonds : angle 5.02296 ( 2826) link_BETA1-4 : bond 0.00449 ( 21) link_BETA1-4 : angle 2.77097 ( 63) link_NAG-ASN : bond 0.00370 ( 33) link_NAG-ASN : angle 2.29258 ( 99) link_NAG-THR : bond 0.00414 ( 3) link_NAG-THR : angle 1.57653 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.4853 (p) REVERT: A 153 MET cc_start: 0.1814 (tpt) cc_final: -0.0523 (mpm) REVERT: A 190 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6903 (mtm-85) REVERT: A 304 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7312 (mptp) REVERT: A 387 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 646 ARG cc_start: 0.8507 (mtp85) cc_final: 0.7892 (mtp-110) REVERT: A 675 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: B 675 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6232 (mp10) REVERT: B 790 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8483 (mttt) REVERT: C 153 MET cc_start: 0.1869 (OUTLIER) cc_final: -0.0002 (mpt) REVERT: C 646 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8284 (mtp85) REVERT: C 675 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6371 (mp10) outliers start: 64 outliers final: 37 residues processed: 227 average time/residue: 0.4941 time to fit residues: 136.4126 Evaluate side-chains 207 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 39 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN B 955 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.198324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160432 restraints weight = 27606.261| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.60 r_work: 0.3405 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26190 Z= 0.226 Angle : 0.639 9.049 35739 Z= 0.321 Chirality : 0.047 0.218 4179 Planarity : 0.004 0.040 4500 Dihedral : 5.617 38.674 4557 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 2.63 % Allowed : 11.62 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3111 helix: 1.83 (0.18), residues: 738 sheet: 0.42 (0.20), residues: 621 loop : -0.88 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.020 0.002 TYR A1067 PHE 0.018 0.002 PHE A 898 TRP 0.008 0.002 TRP C 353 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00549 (26097) covalent geometry : angle 0.60923 (35499) SS BOND : bond 0.00365 ( 36) SS BOND : angle 1.71871 ( 72) hydrogen bonds : bond 0.05045 ( 1008) hydrogen bonds : angle 5.25050 ( 2826) link_BETA1-4 : bond 0.00411 ( 21) link_BETA1-4 : angle 2.87710 ( 63) link_NAG-ASN : bond 0.00411 ( 33) link_NAG-ASN : angle 2.54921 ( 99) link_NAG-THR : bond 0.00569 ( 3) link_NAG-THR : angle 2.08642 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 189 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5149 (OUTLIER) cc_final: 0.4613 (p) REVERT: A 153 MET cc_start: 0.1630 (tpt) cc_final: -0.0896 (mpm) REVERT: A 190 ARG cc_start: 0.7402 (mtt90) cc_final: 0.6958 (mtm-85) REVERT: A 269 TYR cc_start: 0.8399 (m-80) cc_final: 0.7940 (m-80) REVERT: A 646 ARG cc_start: 0.8703 (mtp85) cc_final: 0.7967 (mtp-110) REVERT: A 675 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6046 (mp10) REVERT: B 603 ASN cc_start: 0.8277 (p0) cc_final: 0.7772 (m110) REVERT: B 675 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6079 (mp10) REVERT: B 790 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8616 (mttt) REVERT: B 1045 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8543 (mppt) REVERT: C 153 MET cc_start: 0.1783 (OUTLIER) cc_final: -0.0189 (mpt) REVERT: C 269 TYR cc_start: 0.8405 (m-80) cc_final: 0.8176 (m-80) REVERT: C 646 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8436 (mtp85) REVERT: C 675 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6148 (mp10) outliers start: 73 outliers final: 38 residues processed: 239 average time/residue: 0.4784 time to fit residues: 139.4903 Evaluate side-chains 225 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 100 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 6 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1119 ASN B 207 HIS B 280 ASN B 360 ASN B 474 GLN B1119 ASN C 207 HIS C 474 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.201181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161731 restraints weight = 27789.676| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.62 r_work: 0.3502 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26190 Z= 0.115 Angle : 0.564 8.651 35739 Z= 0.282 Chirality : 0.043 0.209 4179 Planarity : 0.004 0.038 4500 Dihedral : 5.256 38.403 4557 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.70 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 12.73 % Favored : 85.57 % 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 aren not related in a simple way. whole: 0.19 (0.15), residues: 3111 helix: 2.05 (0.19), residues: 738 sheet: 0.44 (0.20), residues: 648 loop : -0.88 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.016 0.001 TYR C 660 PHE 0.016 0.001 PHE B 201 TRP 0.010 0.001 TRP B 633 HIS 0.002 0.000 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00258 (26097) covalent geometry : angle 0.53705 (35499) SS BOND : bond 0.00193 ( 36) SS BOND : angle 1.42989 ( 72) hydrogen bonds : bond 0.04083 ( 1008) hydrogen bonds : angle 4.99024 ( 2826) link_BETA1-4 : bond 0.00455 ( 21) link_BETA1-4 : angle 2.68894 ( 63) link_NAG-ASN : bond 0.00342 ( 33) link_NAG-ASN : angle 2.27730 ( 99) link_NAG-THR : bond 0.00286 ( 3) link_NAG-THR : angle 1.93928 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2139 (OUTLIER) cc_final: -0.0317 (mpm) REVERT: A 190 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6847 (mtm-85) REVERT: A 269 TYR cc_start: 0.7972 (m-80) cc_final: 0.7770 (m-80) REVERT: A 646 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7874 (mtp-110) REVERT: A 675 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6175 (mp10) REVERT: B 153 MET cc_start: 0.2070 (tpt) cc_final: 0.0002 (mpt) REVERT: B 675 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6288 (mp10) REVERT: B 790 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: C 153 MET cc_start: 0.2066 (OUTLIER) cc_final: 0.0220 (mpt) REVERT: C 646 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8064 (mtp85) REVERT: C 675 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6344 (mp10) outliers start: 47 outliers final: 29 residues processed: 211 average time/residue: 0.4383 time to fit residues: 113.1057 Evaluate side-chains 205 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 98 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 321 GLN B 207 HIS B 360 ASN ** C 280 ASN ** 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 = 0.4187 r_free = 0.4187 target = 0.200519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161290 restraints weight = 27752.481| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.59 r_work: 0.3482 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26190 Z= 0.138 Angle : 0.572 8.307 35739 Z= 0.286 Chirality : 0.044 0.211 4179 Planarity : 0.004 0.040 4500 Dihedral : 5.143 37.389 4557 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.86 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 12.63 % Favored : 85.50 % 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 aren not related in a simple way. whole: 0.23 (0.15), residues: 3111 helix: 2.08 (0.19), residues: 738 sheet: 0.43 (0.20), residues: 645 loop : -0.84 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.026 0.001 TYR B 170 PHE 0.015 0.001 PHE A 898 TRP 0.010 0.001 TRP A 633 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00324 (26097) covalent geometry : angle 0.54500 (35499) SS BOND : bond 0.00227 ( 36) SS BOND : angle 1.47534 ( 72) hydrogen bonds : bond 0.04255 ( 1008) hydrogen bonds : angle 4.98528 ( 2826) link_BETA1-4 : bond 0.00420 ( 21) link_BETA1-4 : angle 2.69216 ( 63) link_NAG-ASN : bond 0.00356 ( 33) link_NAG-ASN : angle 2.26787 ( 99) link_NAG-THR : bond 0.00449 ( 3) link_NAG-THR : angle 1.72263 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5448 (OUTLIER) cc_final: 0.4974 (p) REVERT: A 153 MET cc_start: 0.2199 (tpt) cc_final: -0.0415 (mpm) REVERT: A 190 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6858 (mtm-85) REVERT: A 646 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7862 (mtp-110) REVERT: A 675 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: B 153 MET cc_start: 0.2083 (tpt) cc_final: 0.0020 (mpt) REVERT: B 675 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6303 (mp10) REVERT: B 790 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: C 153 MET cc_start: 0.2060 (OUTLIER) cc_final: 0.0247 (mpt) REVERT: C 646 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: C 675 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6314 (mp10) outliers start: 52 outliers final: 35 residues processed: 217 average time/residue: 0.4493 time to fit residues: 119.4521 Evaluate side-chains 213 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 270 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 305 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 360 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.197074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157261 restraints weight = 27771.431| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.63 r_work: 0.3303 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 26190 Z= 0.271 Angle : 0.671 8.927 35739 Z= 0.338 Chirality : 0.048 0.222 4179 Planarity : 0.005 0.041 4500 Dihedral : 5.595 37.552 4557 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.41 % Favored : 96.40 % Rotamer: Outliers : 1.91 % Allowed : 12.70 % Favored : 85.39 % 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 aren not related in a simple way. whole: -0.05 (0.14), residues: 3111 helix: 1.73 (0.18), residues: 738 sheet: 0.40 (0.20), residues: 642 loop : -1.02 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.024 0.002 TYR C 170 PHE 0.019 0.002 PHE C 541 TRP 0.014 0.002 TRP A 353 HIS 0.008 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00662 (26097) covalent geometry : angle 0.64238 (35499) SS BOND : bond 0.00457 ( 36) SS BOND : angle 1.78157 ( 72) hydrogen bonds : bond 0.05276 ( 1008) hydrogen bonds : angle 5.25283 ( 2826) link_BETA1-4 : bond 0.00362 ( 21) link_BETA1-4 : angle 2.84034 ( 63) link_NAG-ASN : bond 0.00402 ( 33) link_NAG-ASN : angle 2.62395 ( 99) link_NAG-THR : bond 0.00670 ( 3) link_NAG-THR : angle 2.15438 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5244 (OUTLIER) cc_final: 0.4728 (p) REVERT: A 153 MET cc_start: 0.1613 (OUTLIER) cc_final: -0.0736 (mpm) REVERT: A 190 ARG cc_start: 0.7528 (mtt90) cc_final: 0.6977 (mtm-85) REVERT: A 646 ARG cc_start: 0.8611 (mtp85) cc_final: 0.7945 (mtp-110) REVERT: A 675 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.5938 (mp10) REVERT: B 153 MET cc_start: 0.1494 (tpt) cc_final: -0.0224 (mpt) REVERT: B 675 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.5860 (mp10) REVERT: B 790 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (mttt) REVERT: C 59 PHE cc_start: 0.8751 (m-10) cc_final: 0.8517 (m-10) REVERT: C 153 MET cc_start: 0.1650 (OUTLIER) cc_final: -0.0134 (mpt) REVERT: C 646 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8016 (mtp-110) REVERT: C 675 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.5884 (mp10) outliers start: 53 outliers final: 38 residues processed: 226 average time/residue: 0.4219 time to fit residues: 118.6013 Evaluate side-chains 230 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 292 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A1119 ASN B 207 HIS B 280 ASN B1119 ASN C 207 HIS C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.200331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159597 restraints weight = 27506.070| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.69 r_work: 0.3474 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26190 Z= 0.130 Angle : 0.575 8.631 35739 Z= 0.288 Chirality : 0.044 0.309 4179 Planarity : 0.004 0.040 4500 Dihedral : 5.225 38.803 4557 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 1.73 % Allowed : 13.13 % Favored : 85.14 % 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 aren not related in a simple way. whole: 0.11 (0.15), residues: 3111 helix: 1.93 (0.19), residues: 738 sheet: 0.43 (0.20), residues: 645 loop : -0.92 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.031 0.001 TYR A 170 PHE 0.015 0.001 PHE B 201 TRP 0.010 0.001 TRP A 633 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00302 (26097) covalent geometry : angle 0.54823 (35499) SS BOND : bond 0.00214 ( 36) SS BOND : angle 1.49098 ( 72) hydrogen bonds : bond 0.04196 ( 1008) hydrogen bonds : angle 4.98135 ( 2826) link_BETA1-4 : bond 0.00410 ( 21) link_BETA1-4 : angle 2.64131 ( 63) link_NAG-ASN : bond 0.00343 ( 33) link_NAG-ASN : angle 2.29641 ( 99) link_NAG-THR : bond 0.00436 ( 3) link_NAG-THR : angle 1.45366 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7817.45 seconds wall clock time: 134 minutes 25.82 seconds (8065.82 seconds total)