Starting phenix.real_space_refine on Fri Sep 19 11:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.map" model { file = "/net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eln_48156/09_2025/9eln_48156.cif" } resolution = 2.93 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= 0.021 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 16245 2.51 5 N 4139 2.21 5 O 4951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 25446 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8270 Classifications: {'peptide': 1054} Link IDs: {'PTRANS': 56, 'TRANS': 997} Chain breaks: 6 Chain: "B" Number of atoms: 8157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8157 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 989} Chain breaks: 10 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 8256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8256 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "Q" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.26, per 1000 atoms: 0.25 Number of scatterers: 25446 At special positions: 0 Unit cell: (130.676, 132.83, 197.45, 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 4951 8.00 N 4139 7.00 C 16245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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=2.04 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=2.02 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=2.45 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 343 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 906.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 39 sheets defined 27.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.584A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.207A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.536A 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 438 through 443 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 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.355A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.230A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.983A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.773A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.796A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.641A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.587A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.515A pdb=" N ARG B 498 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.521A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.977A 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 1033 removed outlier: 4.189A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1149 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.092A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.267A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.741A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 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 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.979A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.764A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1139 through 1150 removed outlier: 3.632A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.882A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.404A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.775A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.770A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.622A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.698A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.537A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.716A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.716A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.544A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.942A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.701A pdb=" N VAL B 62 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.736A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.513A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.462A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.411A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 403 removed outlier: 4.085A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.556A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.814A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.692A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.625A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.868A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 63 through 64 removed outlier: 5.487A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.955A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.371A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.268A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.713A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.063A 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: 6.614A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.614A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.392A 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: 4.666A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.28: 4082 1.28 - 1.65: 21815 1.65 - 2.01: 139 2.01 - 2.38: 0 2.38 - 2.74: 1 Bond restraints: 26037 Sorted by residual: bond pdb=" CB PRO C 892 " pdb=" CG PRO C 892 " ideal model delta sigma weight residual 1.492 2.745 -1.253 5.00e-02 4.00e+02 6.28e+02 bond pdb=" CG PRO A 499 " pdb=" CD PRO A 499 " ideal model delta sigma weight residual 1.503 0.920 0.583 3.40e-02 8.65e+02 2.94e+02 bond pdb=" CG PRO C 892 " pdb=" CD PRO C 892 " ideal model delta sigma weight residual 1.503 0.967 0.536 3.40e-02 8.65e+02 2.48e+02 bond pdb=" N PRO C 892 " pdb=" CD PRO C 892 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.80e+01 bond pdb=" N PRO A 499 " pdb=" CD PRO A 499 " ideal model delta sigma weight residual 1.473 1.592 -0.119 1.40e-02 5.10e+03 7.24e+01 ... (remaining 26032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 35405 21.21 - 42.43: 3 42.43 - 63.64: 1 63.64 - 84.86: 0 84.86 - 106.07: 1 Bond angle restraints: 35410 Sorted by residual: angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 111.92 158.66 -46.74 1.34e+00 5.57e-01 1.22e+03 angle pdb=" CB PRO C 892 " pdb=" CG PRO C 892 " pdb=" CD PRO C 892 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" C CYS A 525 " pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sigma weight residual 111.63 72.58 39.05 1.36e+00 5.41e-01 8.24e+02 angle pdb=" N PRO A 499 " pdb=" CD PRO A 499 " pdb=" CG PRO A 499 " ideal model delta sigma weight residual 103.20 67.70 35.50 1.50e+00 4.44e-01 5.60e+02 angle pdb=" CA PRO B1069 " pdb=" N PRO B1069 " pdb=" CD PRO B1069 " ideal model delta sigma weight residual 112.00 93.81 18.19 1.40e+00 5.10e-01 1.69e+02 ... (remaining 35405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 15331 21.38 - 42.76: 596 42.76 - 64.14: 172 64.14 - 85.53: 81 85.53 - 106.91: 35 Dihedral angle restraints: 16215 sinusoidal: 7050 harmonic: 9165 Sorted by residual: dihedral pdb=" CD ARG B 847 " pdb=" NE ARG B 847 " pdb=" CZ ARG B 847 " pdb=" NH1 ARG B 847 " ideal model delta sinusoidal sigma weight residual 0.00 -78.86 78.86 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -162.72 76.72 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 167.15 -74.15 1 1.00e+01 1.00e-02 6.98e+01 ... (remaining 16212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 4141 0.280 - 0.561: 12 0.561 - 0.841: 1 0.841 - 1.121: 0 1.121 - 1.401: 1 Chirality restraints: 4155 Sorted by residual: chirality pdb=" CA CYS A 525 " pdb=" N CYS A 525 " pdb=" C CYS A 525 " pdb=" CB CYS A 525 " both_signs ideal model delta sigma weight residual False 2.51 1.11 1.40 2.00e-01 2.50e+01 4.91e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ARG B 273 " pdb=" N ARG B 273 " pdb=" C ARG B 273 " pdb=" CB ARG B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 4152 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 30 " -0.063 2.00e-02 2.50e+03 2.68e-01 8.96e+02 pdb=" CG ASN A 30 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 30 " -0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN A 30 " 0.469 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 30 " -0.086 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" CG ASN B 30 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 30 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 30 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 847 " 0.967 9.50e-02 1.11e+02 4.34e-01 1.20e+02 pdb=" NE ARG B 847 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 847 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 847 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 847 " 0.006 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 12 2.21 - 2.88: 9424 2.88 - 3.56: 34587 3.56 - 4.23: 59139 4.23 - 4.90: 100317 Nonbonded interactions: 203479 Sorted by model distance: nonbonded pdb=" O THR C 29 " pdb=" OD1 ASN C 30 " model vdw 1.539 3.040 nonbonded pdb=" O PHE B 490 " pdb=" OH TYR B 495 " model vdw 1.667 3.040 nonbonded pdb=" O CYS A 525 " pdb=" CB CYS A 525 " model vdw 1.891 2.752 nonbonded pdb=" CE2 PHE C 377 " pdb=" CG2 THR C 385 " model vdw 1.963 3.760 nonbonded pdb=" O PRO B 426 " pdb=" CE2 PHE B 429 " model vdw 2.041 3.340 ... (remaining 203474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 65 or resid 69 through 72 or resid 81 through 1 \ 38 or resid 154 through 172 or resid 188 through 210 or resid 215 through 358 or \ resid 360 through 387 or resid 391 through 450 or (resid 451 and (name N or nam \ e CA or name C or name O or name CB )) or resid 452 through 507 or (resid 508 th \ rough 509 and (name N or name CA or name C or name O or name CB )) or resid 510 \ through 676 or resid 689 through 837 or resid 852 through 1305)) selection = (chain 'B' and (resid 26 through 138 or resid 154 through 676 or resid 689 throu \ gh 837 or resid 852 through 1305)) selection = (chain 'C' and (resid 26 through 72 or resid 81 through 138 or resid 154 through \ 172 or resid 188 through 210 or resid 215 through 358 or resid 360 through 387 \ or resid 391 through 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 through 507 or (resid 508 through 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'N' 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: 11.120 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: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.200 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.012 1.253 26131 Z= 0.434 Angle : 1.409 106.075 35654 Z= 0.763 Chirality : 0.069 1.401 4155 Planarity : 0.011 0.434 4491 Dihedral : 14.553 106.907 10203 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 0.25 % Allowed : 8.42 % Favored : 91.32 % Cbeta Deviations : 0.14 % 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: 0.54 (0.14), residues: 3100 helix: 1.28 (0.18), residues: 714 sheet: 1.13 (0.20), residues: 600 loop : -0.26 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG B 847 TYR 0.026 0.003 TYR B 380 PHE 0.064 0.003 PHE A 392 TRP 0.033 0.003 TRP C 452 HIS 0.022 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01185 (26037) covalent geometry : angle 1.36806 (35410) SS BOND : bond 0.06807 ( 38) SS BOND : angle 5.37291 ( 76) hydrogen bonds : bond 0.13450 ( 1019) hydrogen bonds : angle 7.66032 ( 2901) link_BETA1-4 : bond 0.00455 ( 21) link_BETA1-4 : angle 1.72500 ( 63) link_NAG-ASN : bond 0.00439 ( 35) link_NAG-ASN : angle 4.51643 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 537 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.7516 (p0) cc_final: 0.7106 (t160) REVERT: A 203 ILE cc_start: 0.8319 (mt) cc_final: 0.8003 (tt) REVERT: A 396 TYR cc_start: 0.7558 (m-80) cc_final: 0.6916 (m-80) REVERT: A 627 ASP cc_start: 0.7955 (t0) cc_final: 0.7699 (t70) REVERT: B 127 PHE cc_start: 0.5727 (m-10) cc_final: 0.5434 (m-80) REVERT: B 192 PHE cc_start: 0.6423 (m-80) cc_final: 0.5950 (m-10) REVERT: B 568 ASP cc_start: 0.8428 (m-30) cc_final: 0.8182 (m-30) REVERT: B 676 THR cc_start: 0.8214 (m) cc_final: 0.8012 (p) REVERT: B 775 ASP cc_start: 0.8348 (m-30) cc_final: 0.8094 (m-30) REVERT: B 1101 HIS cc_start: 0.8105 (m90) cc_final: 0.7825 (m90) REVERT: C 65 PHE cc_start: 0.7455 (m-80) cc_final: 0.6839 (m-10) REVERT: C 153 MET cc_start: 0.1485 (ptm) cc_final: -0.0299 (mpm) REVERT: C 237 ARG cc_start: 0.8337 (mtm180) cc_final: 0.8105 (mtp85) REVERT: C 375 PHE cc_start: 0.7714 (t80) cc_final: 0.7178 (t80) REVERT: C 417 ASN cc_start: 0.6657 (p0) cc_final: 0.6084 (t0) REVERT: C 425 LEU cc_start: 0.8122 (mp) cc_final: 0.7914 (mt) REVERT: C 529 LYS cc_start: 0.7644 (mttt) cc_final: 0.7359 (mmtt) REVERT: C 558 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7941 (mptt) REVERT: C 618 THR cc_start: 0.8685 (m) cc_final: 0.8414 (p) REVERT: C 628 GLN cc_start: 0.7271 (mm110) cc_final: 0.7068 (pt0) REVERT: C 638 THR cc_start: 0.8472 (p) cc_final: 0.7779 (p) REVERT: C 904 TYR cc_start: 0.7904 (t80) cc_final: 0.7573 (t80) REVERT: C 1139 ASP cc_start: 0.8239 (t0) cc_final: 0.7966 (t0) outliers start: 7 outliers final: 1 residues processed: 541 average time/residue: 0.5090 time to fit residues: 327.7341 Evaluate side-chains 298 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 606 ASN A 690 GLN A 755 GLN A 774 GLN A 784 GLN A 804 GLN A 955 ASN A 960 ASN A1005 GLN A1011 GLN B 61 ASN B 474 GLN B 779 GLN B1002 GLN C 196 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 779 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138550 restraints weight = 31303.432| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.13 r_work: 0.3270 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26131 Z= 0.152 Angle : 0.702 19.015 35654 Z= 0.357 Chirality : 0.047 0.406 4155 Planarity : 0.005 0.085 4491 Dihedral : 8.400 64.554 4527 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.83 % Allowed : 12.20 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.69 (0.14), residues: 3100 helix: 2.25 (0.19), residues: 727 sheet: 1.11 (0.20), residues: 619 loop : -0.58 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 847 TYR 0.020 0.002 TYR C 453 PHE 0.030 0.002 PHE A 392 TRP 0.032 0.002 TRP C 452 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00343 (26037) covalent geometry : angle 0.66096 (35410) SS BOND : bond 0.00404 ( 38) SS BOND : angle 1.70799 ( 76) hydrogen bonds : bond 0.04762 ( 1019) hydrogen bonds : angle 6.11744 ( 2901) link_BETA1-4 : bond 0.00740 ( 21) link_BETA1-4 : angle 2.16524 ( 63) link_NAG-ASN : bond 0.00593 ( 35) link_NAG-ASN : angle 3.87195 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8083 (mt) cc_final: 0.7802 (tt) REVERT: A 349 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 396 TYR cc_start: 0.7881 (m-80) cc_final: 0.7530 (m-80) REVERT: A 571 ASP cc_start: 0.8010 (t70) cc_final: 0.7723 (t0) REVERT: A 591 SER cc_start: 0.8723 (t) cc_final: 0.8451 (m) REVERT: A 625 HIS cc_start: 0.8055 (m-70) cc_final: 0.7721 (m-70) REVERT: A 654 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 740 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7667 (ttt) REVERT: B 195 LYS cc_start: 0.7469 (tmmt) cc_final: 0.7130 (tmmt) REVERT: B 202 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7203 (mttt) REVERT: B 568 ASP cc_start: 0.8527 (m-30) cc_final: 0.8236 (m-30) REVERT: B 619 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 775 ASP cc_start: 0.8284 (m-30) cc_final: 0.8062 (m-30) REVERT: B 790 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8611 (mmtt) REVERT: B 935 GLN cc_start: 0.8167 (tt0) cc_final: 0.7875 (tt0) REVERT: B 1002 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: B 1101 HIS cc_start: 0.8034 (m90) cc_final: 0.7775 (m90) REVERT: C 153 MET cc_start: 0.1447 (ptm) cc_final: -0.0410 (mpm) REVERT: C 169 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7148 (mp0) REVERT: C 170 TYR cc_start: 0.8109 (t80) cc_final: 0.7907 (t80) REVERT: C 202 LYS cc_start: 0.8292 (mttm) cc_final: 0.7980 (mttp) REVERT: C 237 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7883 (mtp85) REVERT: C 338 PHE cc_start: 0.7533 (m-80) cc_final: 0.7245 (m-80) REVERT: C 375 PHE cc_start: 0.7911 (t80) cc_final: 0.7400 (t80) REVERT: C 422 ASN cc_start: 0.7433 (m110) cc_final: 0.7033 (p0) REVERT: C 460 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7245 (tptm) REVERT: C 529 LYS cc_start: 0.7736 (mttt) cc_final: 0.7220 (tppt) REVERT: C 574 ASP cc_start: 0.7513 (p0) cc_final: 0.6758 (m-30) REVERT: C 618 THR cc_start: 0.8798 (m) cc_final: 0.8521 (p) REVERT: C 904 TYR cc_start: 0.7718 (t80) cc_final: 0.7400 (t80) REVERT: C 1005 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: C 1010 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7985 (mm-40) outliers start: 78 outliers final: 30 residues processed: 376 average time/residue: 0.4683 time to fit residues: 214.6460 Evaluate side-chains 297 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 505 HIS A 960 ASN B 61 ASN B 321 GLN B 487 ASN B 703 ASN B1002 GLN C 137 ASN C 196 ASN C 280 ASN C 321 GLN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 644 GLN C 774 GLN C1125 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123104 restraints weight = 31138.124| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.25 r_work: 0.3244 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26131 Z= 0.162 Angle : 0.636 17.898 35654 Z= 0.324 Chirality : 0.047 0.416 4155 Planarity : 0.004 0.063 4491 Dihedral : 6.035 54.560 4527 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.27 % Allowed : 13.03 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.53 (0.14), residues: 3100 helix: 2.30 (0.19), residues: 718 sheet: 1.00 (0.20), residues: 619 loop : -0.76 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 847 TYR 0.020 0.001 TYR C 351 PHE 0.028 0.002 PHE A 392 TRP 0.020 0.002 TRP C 452 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00372 (26037) covalent geometry : angle 0.60203 (35410) SS BOND : bond 0.00550 ( 38) SS BOND : angle 1.44581 ( 76) hydrogen bonds : bond 0.04686 ( 1019) hydrogen bonds : angle 5.77161 ( 2901) link_BETA1-4 : bond 0.00685 ( 21) link_BETA1-4 : angle 1.98644 ( 63) link_NAG-ASN : bond 0.00450 ( 35) link_NAG-ASN : angle 3.32365 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7082 (mtpt) REVERT: A 349 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7998 (p) REVERT: A 396 TYR cc_start: 0.8101 (m-80) cc_final: 0.7717 (m-80) REVERT: A 493 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7011 (tp40) REVERT: A 571 ASP cc_start: 0.8055 (t70) cc_final: 0.7694 (t0) REVERT: A 591 SER cc_start: 0.8946 (t) cc_final: 0.8659 (m) REVERT: A 625 HIS cc_start: 0.8157 (m-70) cc_final: 0.7763 (m-70) REVERT: A 654 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 921 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8088 (mtpm) REVERT: B 126 VAL cc_start: 0.5964 (m) cc_final: 0.5299 (p) REVERT: B 195 LYS cc_start: 0.7677 (tmmt) cc_final: 0.7260 (tmmt) REVERT: B 207 HIS cc_start: 0.7922 (t70) cc_final: 0.7713 (t70) REVERT: B 304 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7501 (mptt) REVERT: B 619 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: B 775 ASP cc_start: 0.8539 (m-30) cc_final: 0.8265 (m-30) REVERT: B 916 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 1101 HIS cc_start: 0.8257 (m90) cc_final: 0.7902 (m90) REVERT: B 1142 GLN cc_start: 0.7150 (tp40) cc_final: 0.6631 (tm-30) REVERT: C 153 MET cc_start: 0.1519 (ptm) cc_final: -0.0422 (mpm) REVERT: C 169 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7388 (mp0) REVERT: C 170 TYR cc_start: 0.8099 (t80) cc_final: 0.7885 (t80) REVERT: C 202 LYS cc_start: 0.8323 (mttm) cc_final: 0.8018 (mttp) REVERT: C 375 PHE cc_start: 0.8119 (t80) cc_final: 0.7625 (t80) REVERT: C 452 TRP cc_start: 0.5844 (p90) cc_final: 0.5609 (p-90) REVERT: C 460 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7280 (tptm) REVERT: C 529 LYS cc_start: 0.8008 (mttt) cc_final: 0.7381 (tppt) REVERT: C 618 THR cc_start: 0.8894 (m) cc_final: 0.8615 (p) REVERT: C 904 TYR cc_start: 0.7948 (t80) cc_final: 0.7540 (t80) REVERT: C 983 ARG cc_start: 0.7834 (mtm110) cc_final: 0.6972 (mtm-85) REVERT: C 1010 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8086 (mm-40) REVERT: C 1107 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7774 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8431 (t0) cc_final: 0.8176 (t0) REVERT: C 1141 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7135 (mt) outliers start: 90 outliers final: 41 residues processed: 347 average time/residue: 0.4977 time to fit residues: 208.9216 Evaluate side-chains 298 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 71 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 505 HIS A 960 ASN B 61 ASN B 134 GLN B 321 GLN B 703 ASN B 954 HIS C 61 ASN C 280 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 779 GLN C 914 ASN C1119 ASN C1125 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122590 restraints weight = 31017.520| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.03 r_work: 0.3252 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26131 Z= 0.137 Angle : 0.599 16.492 35654 Z= 0.303 Chirality : 0.045 0.391 4155 Planarity : 0.004 0.056 4491 Dihedral : 5.312 54.130 4526 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.45 % Allowed : 13.32 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.47 (0.15), residues: 3100 helix: 2.40 (0.19), residues: 711 sheet: 0.84 (0.20), residues: 647 loop : -0.82 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 847 TYR 0.021 0.001 TYR A 170 PHE 0.028 0.001 PHE A 392 TRP 0.016 0.001 TRP A 452 HIS 0.007 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00316 (26037) covalent geometry : angle 0.56478 (35410) SS BOND : bond 0.00383 ( 38) SS BOND : angle 1.23608 ( 76) hydrogen bonds : bond 0.04261 ( 1019) hydrogen bonds : angle 5.63832 ( 2901) link_BETA1-4 : bond 0.00610 ( 21) link_BETA1-4 : angle 1.82134 ( 63) link_NAG-ASN : bond 0.00443 ( 35) link_NAG-ASN : angle 3.33051 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 268 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6986 (mttm) REVERT: A 349 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8066 (p) REVERT: A 571 ASP cc_start: 0.8058 (t70) cc_final: 0.7679 (t0) REVERT: A 591 SER cc_start: 0.8899 (t) cc_final: 0.8602 (m) REVERT: A 625 HIS cc_start: 0.8123 (m-70) cc_final: 0.7741 (m-70) REVERT: A 654 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 921 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8094 (mtpm) REVERT: B 126 VAL cc_start: 0.6149 (m) cc_final: 0.5508 (p) REVERT: B 168 PHE cc_start: 0.5711 (m-80) cc_final: 0.5334 (m-80) REVERT: B 195 LYS cc_start: 0.7741 (tmmt) cc_final: 0.7394 (tmmt) REVERT: B 304 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7562 (mptt) REVERT: B 619 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: B 745 ASP cc_start: 0.6683 (p0) cc_final: 0.6427 (p0) REVERT: B 759 PHE cc_start: 0.7835 (t80) cc_final: 0.7181 (m-80) REVERT: B 775 ASP cc_start: 0.8509 (m-30) cc_final: 0.8256 (m-30) REVERT: B 776 LYS cc_start: 0.8566 (tttm) cc_final: 0.8313 (tttm) REVERT: B 780 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 916 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 1101 HIS cc_start: 0.8253 (m90) cc_final: 0.7952 (m90) REVERT: B 1142 GLN cc_start: 0.7153 (tp40) cc_final: 0.6659 (tm-30) REVERT: C 153 MET cc_start: 0.1592 (ptm) cc_final: -0.0284 (mpm) REVERT: C 169 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7459 (mp0) REVERT: C 375 PHE cc_start: 0.8185 (t80) cc_final: 0.7724 (t80) REVERT: C 460 LYS cc_start: 0.7780 (mmtp) cc_final: 0.7304 (tptm) REVERT: C 529 LYS cc_start: 0.7969 (mttt) cc_final: 0.7376 (tppt) REVERT: C 618 THR cc_start: 0.8949 (m) cc_final: 0.8667 (p) REVERT: C 634 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8428 (mpt180) REVERT: C 904 TYR cc_start: 0.7940 (t80) cc_final: 0.7564 (t80) REVERT: C 1010 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8066 (mm-40) REVERT: C 1107 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7737 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8449 (t0) cc_final: 0.8173 (t0) REVERT: C 1141 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7216 (mt) outliers start: 95 outliers final: 48 residues processed: 338 average time/residue: 0.5201 time to fit residues: 211.0047 Evaluate side-chains 307 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 23 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120412 restraints weight = 31096.180| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.05 r_work: 0.3210 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26131 Z= 0.167 Angle : 0.606 15.740 35654 Z= 0.309 Chirality : 0.046 0.412 4155 Planarity : 0.004 0.054 4491 Dihedral : 5.174 56.111 4526 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.67 % Allowed : 13.21 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.14), residues: 3100 helix: 2.36 (0.19), residues: 713 sheet: 0.71 (0.20), residues: 626 loop : -0.92 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR B1067 PHE 0.035 0.002 PHE A 392 TRP 0.030 0.002 TRP A 452 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00397 (26037) covalent geometry : angle 0.57640 (35410) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.35771 ( 76) hydrogen bonds : bond 0.04448 ( 1019) hydrogen bonds : angle 5.62640 ( 2901) link_BETA1-4 : bond 0.00596 ( 21) link_BETA1-4 : angle 1.61035 ( 63) link_NAG-ASN : bond 0.00419 ( 35) link_NAG-ASN : angle 3.14698 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 243 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6810 (mmtm) REVERT: A 349 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 493 GLN cc_start: 0.7474 (tt0) cc_final: 0.6900 (tp40) REVERT: A 571 ASP cc_start: 0.8084 (t70) cc_final: 0.7638 (t0) REVERT: A 591 SER cc_start: 0.8933 (t) cc_final: 0.8664 (m) REVERT: A 625 HIS cc_start: 0.8114 (m-70) cc_final: 0.7703 (m-70) REVERT: A 654 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 921 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8100 (mtpm) REVERT: B 168 PHE cc_start: 0.5798 (m-80) cc_final: 0.5356 (m-80) REVERT: B 195 LYS cc_start: 0.7799 (tmmt) cc_final: 0.7353 (tmmt) REVERT: B 273 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6567 (mmp-170) REVERT: B 304 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7482 (mptt) REVERT: B 619 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 745 ASP cc_start: 0.6894 (p0) cc_final: 0.6649 (p0) REVERT: B 759 PHE cc_start: 0.7836 (t80) cc_final: 0.7137 (m-80) REVERT: B 775 ASP cc_start: 0.8606 (m-30) cc_final: 0.8360 (m-30) REVERT: B 776 LYS cc_start: 0.8669 (tttm) cc_final: 0.8422 (tttm) REVERT: B 916 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8610 (tp) REVERT: B 1101 HIS cc_start: 0.8325 (m90) cc_final: 0.7955 (m90) REVERT: B 1142 GLN cc_start: 0.7105 (tp40) cc_final: 0.6578 (tm-30) REVERT: C 153 MET cc_start: 0.1498 (ptm) cc_final: -0.0242 (mpm) REVERT: C 375 PHE cc_start: 0.8356 (t80) cc_final: 0.7891 (t80) REVERT: C 460 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7347 (tptm) REVERT: C 529 LYS cc_start: 0.8080 (mttt) cc_final: 0.7390 (tppt) REVERT: C 904 TYR cc_start: 0.7928 (t80) cc_final: 0.7566 (t80) REVERT: C 918 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: C 984 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7945 (mm) REVERT: C 1010 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 1139 ASP cc_start: 0.8423 (t0) cc_final: 0.8108 (t0) REVERT: C 1141 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7131 (mt) outliers start: 101 outliers final: 49 residues processed: 322 average time/residue: 0.5298 time to fit residues: 204.3696 Evaluate side-chains 291 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 301 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS C 61 ASN C 239 GLN C 280 ASN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C1125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131979 restraints weight = 30965.513| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.20 r_work: 0.3162 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26131 Z= 0.137 Angle : 0.589 14.843 35654 Z= 0.300 Chirality : 0.045 0.385 4155 Planarity : 0.004 0.052 4491 Dihedral : 5.087 54.665 4526 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.23 % Allowed : 14.16 % Favored : 82.61 % 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: 0.31 (0.15), residues: 3100 helix: 2.37 (0.19), residues: 714 sheet: 0.68 (0.20), residues: 638 loop : -0.95 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.001 PHE A 392 TRP 0.039 0.002 TRP A 452 HIS 0.007 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00320 (26037) covalent geometry : angle 0.55791 (35410) SS BOND : bond 0.00412 ( 38) SS BOND : angle 1.84177 ( 76) hydrogen bonds : bond 0.04188 ( 1019) hydrogen bonds : angle 5.56384 ( 2901) link_BETA1-4 : bond 0.00558 ( 21) link_BETA1-4 : angle 1.51715 ( 63) link_NAG-ASN : bond 0.00396 ( 35) link_NAG-ASN : angle 2.96991 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 242 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7099 (mmtm) REVERT: A 349 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8049 (p) REVERT: A 493 GLN cc_start: 0.7503 (tt0) cc_final: 0.7041 (tp40) REVERT: A 571 ASP cc_start: 0.8058 (t70) cc_final: 0.7637 (t0) REVERT: A 591 SER cc_start: 0.8901 (t) cc_final: 0.8651 (m) REVERT: A 625 HIS cc_start: 0.8035 (m-70) cc_final: 0.7716 (m-70) REVERT: A 654 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: A 740 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7627 (tmt) REVERT: A 921 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8089 (mtpm) REVERT: B 168 PHE cc_start: 0.5810 (m-80) cc_final: 0.5501 (m-80) REVERT: B 195 LYS cc_start: 0.7817 (tmmt) cc_final: 0.7457 (tmmt) REVERT: B 273 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6661 (mmp-170) REVERT: B 304 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7563 (mptt) REVERT: B 619 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 745 ASP cc_start: 0.6931 (p0) cc_final: 0.6640 (p0) REVERT: B 775 ASP cc_start: 0.8412 (m-30) cc_final: 0.8203 (m-30) REVERT: B 916 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8541 (tp) REVERT: B 1101 HIS cc_start: 0.8239 (m90) cc_final: 0.8019 (m90) REVERT: B 1142 GLN cc_start: 0.7197 (tp40) cc_final: 0.6741 (tm-30) REVERT: C 153 MET cc_start: 0.1511 (ptm) cc_final: -0.0197 (mpm) REVERT: C 375 PHE cc_start: 0.8328 (t80) cc_final: 0.7817 (t80) REVERT: C 452 TRP cc_start: 0.6096 (p-90) cc_final: 0.5851 (p90) REVERT: C 460 LYS cc_start: 0.7846 (mmtp) cc_final: 0.7597 (mmtm) REVERT: C 529 LYS cc_start: 0.8051 (mttt) cc_final: 0.7452 (tppt) REVERT: C 634 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (mpt180) REVERT: C 731 MET cc_start: 0.9249 (ptp) cc_final: 0.9039 (ptp) REVERT: C 904 TYR cc_start: 0.7845 (t80) cc_final: 0.7615 (t80) REVERT: C 984 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 1010 GLN cc_start: 0.8250 (mm-40) cc_final: 0.8028 (mm-40) REVERT: C 1139 ASP cc_start: 0.8445 (t0) cc_final: 0.8132 (t0) REVERT: C 1141 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7316 (mt) outliers start: 89 outliers final: 53 residues processed: 313 average time/residue: 0.5134 time to fit residues: 193.7686 Evaluate side-chains 286 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 142 optimal weight: 0.4980 chunk 234 optimal weight: 0.0070 chunk 198 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 26 GLN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.175971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123730 restraints weight = 30956.658| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.24 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26131 Z= 0.117 Angle : 0.573 13.969 35654 Z= 0.292 Chirality : 0.044 0.367 4155 Planarity : 0.004 0.051 4491 Dihedral : 4.941 54.035 4526 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.05 % Allowed : 14.81 % Favored : 82.14 % 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: 0.37 (0.15), residues: 3100 helix: 2.45 (0.19), residues: 714 sheet: 0.69 (0.19), residues: 653 loop : -0.92 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 319 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE A 392 TRP 0.062 0.002 TRP C 452 HIS 0.002 0.000 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00263 (26037) covalent geometry : angle 0.54621 (35410) SS BOND : bond 0.00427 ( 38) SS BOND : angle 1.67309 ( 76) hydrogen bonds : bond 0.03906 ( 1019) hydrogen bonds : angle 5.46607 ( 2901) link_BETA1-4 : bond 0.00553 ( 21) link_BETA1-4 : angle 1.45216 ( 63) link_NAG-ASN : bond 0.00403 ( 35) link_NAG-ASN : angle 2.78810 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 246 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6959 (mmtm) REVERT: A 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: A 349 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7997 (p) REVERT: A 493 GLN cc_start: 0.7406 (tt0) cc_final: 0.6887 (tp40) REVERT: A 571 ASP cc_start: 0.8122 (t70) cc_final: 0.7698 (t0) REVERT: A 591 SER cc_start: 0.8974 (t) cc_final: 0.8709 (m) REVERT: A 625 HIS cc_start: 0.8139 (m-70) cc_final: 0.7761 (m-70) REVERT: A 641 ASN cc_start: 0.8319 (t0) cc_final: 0.8102 (t0) REVERT: A 654 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 164 ASN cc_start: 0.5450 (m-40) cc_final: 0.4856 (t0) REVERT: B 168 PHE cc_start: 0.5728 (m-80) cc_final: 0.5306 (m-80) REVERT: B 195 LYS cc_start: 0.7820 (tmmt) cc_final: 0.7369 (tmmt) REVERT: B 239 GLN cc_start: 0.7475 (tt0) cc_final: 0.6854 (mm110) REVERT: B 273 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6362 (mmp-170) REVERT: B 304 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7489 (mptt) REVERT: B 619 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: B 745 ASP cc_start: 0.6978 (p0) cc_final: 0.6736 (p0) REVERT: B 775 ASP cc_start: 0.8498 (m-30) cc_final: 0.8271 (m-30) REVERT: B 916 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 1101 HIS cc_start: 0.8401 (m90) cc_final: 0.7994 (m90) REVERT: C 153 MET cc_start: 0.1559 (ptm) cc_final: -0.0190 (mpm) REVERT: C 321 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8553 (mm-40) REVERT: C 375 PHE cc_start: 0.8359 (t80) cc_final: 0.7840 (t80) REVERT: C 460 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7627 (mmtm) REVERT: C 529 LYS cc_start: 0.8117 (mttt) cc_final: 0.7409 (tppt) REVERT: C 634 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (mpt180) REVERT: C 731 MET cc_start: 0.9340 (ptp) cc_final: 0.9130 (ptp) REVERT: C 904 TYR cc_start: 0.8049 (t80) cc_final: 0.7671 (t80) REVERT: C 984 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8015 (mm) REVERT: C 1010 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8147 (mm-40) REVERT: C 1107 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8353 (t0) cc_final: 0.7979 (t0) REVERT: C 1141 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7163 (mt) outliers start: 84 outliers final: 40 residues processed: 311 average time/residue: 0.5125 time to fit residues: 191.3266 Evaluate side-chains 274 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 298 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 162 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 61 ASN B 317 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 954 HIS C 137 ASN C 280 ASN C 774 GLN C1125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120309 restraints weight = 31131.508| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.98 r_work: 0.3236 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26131 Z= 0.139 Angle : 0.592 13.773 35654 Z= 0.299 Chirality : 0.045 0.383 4155 Planarity : 0.004 0.053 4491 Dihedral : 5.060 55.312 4526 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.98 % Allowed : 15.21 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3100 helix: 2.43 (0.19), residues: 714 sheet: 0.67 (0.20), residues: 641 loop : -0.95 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 319 TYR 0.018 0.001 TYR C1067 PHE 0.027 0.001 PHE A 392 TRP 0.045 0.002 TRP C 452 HIS 0.007 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00324 (26037) covalent geometry : angle 0.56418 (35410) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.60729 ( 76) hydrogen bonds : bond 0.04073 ( 1019) hydrogen bonds : angle 5.47369 ( 2901) link_BETA1-4 : bond 0.00548 ( 21) link_BETA1-4 : angle 1.44330 ( 63) link_NAG-ASN : bond 0.00396 ( 35) link_NAG-ASN : angle 2.90023 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 239 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7050 (mmtm) REVERT: A 349 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 493 GLN cc_start: 0.7427 (tt0) cc_final: 0.6932 (tp40) REVERT: A 571 ASP cc_start: 0.8089 (t70) cc_final: 0.7730 (t0) REVERT: A 591 SER cc_start: 0.8971 (t) cc_final: 0.8711 (m) REVERT: A 625 HIS cc_start: 0.8088 (m-70) cc_final: 0.7730 (m-70) REVERT: A 641 ASN cc_start: 0.8296 (t0) cc_final: 0.8063 (t160) REVERT: A 654 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 791 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8268 (m) REVERT: B 52 GLN cc_start: 0.8820 (tm130) cc_final: 0.8399 (tp-100) REVERT: B 164 ASN cc_start: 0.5425 (m-40) cc_final: 0.4801 (t0) REVERT: B 168 PHE cc_start: 0.5800 (m-80) cc_final: 0.5417 (m-80) REVERT: B 304 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7569 (mptt) REVERT: B 619 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 745 ASP cc_start: 0.7072 (p0) cc_final: 0.6799 (p0) REVERT: B 916 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (tt) REVERT: B 1101 HIS cc_start: 0.8334 (m90) cc_final: 0.8044 (m90) REVERT: C 153 MET cc_start: 0.1600 (ptm) cc_final: -0.0237 (mpm) REVERT: C 375 PHE cc_start: 0.8356 (t80) cc_final: 0.7859 (t80) REVERT: C 460 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7618 (mmtm) REVERT: C 529 LYS cc_start: 0.8128 (mttt) cc_final: 0.7481 (tppt) REVERT: C 574 ASP cc_start: 0.7413 (p0) cc_final: 0.7110 (p0) REVERT: C 634 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8471 (mpt180) REVERT: C 731 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9072 (ptp) REVERT: C 904 TYR cc_start: 0.7946 (t80) cc_final: 0.7657 (t80) REVERT: C 984 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8146 (mm) REVERT: C 1010 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8131 (mm-40) REVERT: C 1107 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7714 (mtp-110) REVERT: C 1141 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7396 (mt) outliers start: 82 outliers final: 52 residues processed: 304 average time/residue: 0.4926 time to fit residues: 181.2688 Evaluate side-chains 295 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 47 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 208 optimal weight: 0.3980 chunk 303 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 556 ASN C 774 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131945 restraints weight = 31040.732| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.15 r_work: 0.3170 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26131 Z= 0.129 Angle : 0.581 13.275 35654 Z= 0.295 Chirality : 0.045 0.372 4155 Planarity : 0.004 0.051 4491 Dihedral : 5.013 54.582 4526 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 3.01 % Allowed : 15.32 % Favored : 81.67 % 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: 0.31 (0.15), residues: 3100 helix: 2.36 (0.19), residues: 720 sheet: 0.63 (0.20), residues: 645 loop : -0.94 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 319 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE A 32 TRP 0.038 0.002 TRP C 452 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00296 (26037) covalent geometry : angle 0.55632 (35410) SS BOND : bond 0.00388 ( 38) SS BOND : angle 1.52325 ( 76) hydrogen bonds : bond 0.03982 ( 1019) hydrogen bonds : angle 5.44598 ( 2901) link_BETA1-4 : bond 0.00532 ( 21) link_BETA1-4 : angle 1.36907 ( 63) link_NAG-ASN : bond 0.00354 ( 35) link_NAG-ASN : angle 2.75503 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 234 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7095 (mmtm) REVERT: A 349 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 493 GLN cc_start: 0.7447 (tt0) cc_final: 0.6972 (tp40) REVERT: A 569 ILE cc_start: 0.8304 (mm) cc_final: 0.8094 (tp) REVERT: A 571 ASP cc_start: 0.8024 (t70) cc_final: 0.7681 (t0) REVERT: A 591 SER cc_start: 0.8938 (t) cc_final: 0.8695 (m) REVERT: A 625 HIS cc_start: 0.8023 (m-70) cc_final: 0.7695 (m-70) REVERT: A 654 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 791 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8295 (m) REVERT: B 164 ASN cc_start: 0.5351 (m-40) cc_final: 0.4874 (t0) REVERT: B 168 PHE cc_start: 0.5843 (m-80) cc_final: 0.5605 (m-80) REVERT: B 304 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7585 (mptt) REVERT: B 619 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 916 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 153 MET cc_start: 0.1559 (ptm) cc_final: -0.0276 (mpm) REVERT: C 375 PHE cc_start: 0.8363 (t80) cc_final: 0.7884 (t80) REVERT: C 529 LYS cc_start: 0.8036 (mttt) cc_final: 0.7467 (tppt) REVERT: C 574 ASP cc_start: 0.7367 (p0) cc_final: 0.7124 (p0) REVERT: C 634 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8484 (mpt180) REVERT: C 731 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9032 (ptp) REVERT: C 740 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: C 1010 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8058 (mm-40) REVERT: C 1107 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7664 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8430 (t0) cc_final: 0.8115 (t0) REVERT: C 1141 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7359 (mt) outliers start: 83 outliers final: 49 residues processed: 298 average time/residue: 0.4602 time to fit residues: 168.0865 Evaluate side-chains 287 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 193 optimal weight: 0.2980 chunk 197 optimal weight: 0.6980 chunk 300 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 206 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 307 optimal weight: 0.6980 chunk 301 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 954 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 914 ASN C1125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120171 restraints weight = 31196.874| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.01 r_work: 0.3239 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 26131 Z= 0.173 Angle : 0.717 59.189 35654 Z= 0.390 Chirality : 0.048 1.009 4155 Planarity : 0.004 0.051 4491 Dihedral : 5.069 54.576 4526 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 2.58 % Allowed : 15.90 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.30 (0.15), residues: 3100 helix: 2.37 (0.19), residues: 720 sheet: 0.61 (0.19), residues: 653 loop : -0.95 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE A 392 TRP 0.036 0.002 TRP C 452 HIS 0.009 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00377 (26037) covalent geometry : angle 0.69432 (35410) SS BOND : bond 0.00376 ( 38) SS BOND : angle 1.49916 ( 76) hydrogen bonds : bond 0.03971 ( 1019) hydrogen bonds : angle 5.44734 ( 2901) link_BETA1-4 : bond 0.00500 ( 21) link_BETA1-4 : angle 1.42008 ( 63) link_NAG-ASN : bond 0.00412 ( 35) link_NAG-ASN : angle 3.05582 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6959 (mmtm) REVERT: A 349 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 493 GLN cc_start: 0.7399 (tt0) cc_final: 0.6888 (tp40) REVERT: A 569 ILE cc_start: 0.8359 (mm) cc_final: 0.8122 (tp) REVERT: A 571 ASP cc_start: 0.8035 (t70) cc_final: 0.7646 (t0) REVERT: A 591 SER cc_start: 0.8967 (t) cc_final: 0.8706 (m) REVERT: A 625 HIS cc_start: 0.8096 (m-70) cc_final: 0.7712 (m-70) REVERT: A 654 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 791 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8292 (m) REVERT: B 164 ASN cc_start: 0.5306 (m-40) cc_final: 0.4770 (t0) REVERT: B 168 PHE cc_start: 0.5812 (m-80) cc_final: 0.5473 (m-80) REVERT: B 304 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7514 (mptt) REVERT: B 619 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: B 745 ASP cc_start: 0.7026 (p0) cc_final: 0.6792 (p0) REVERT: B 916 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 153 MET cc_start: 0.1592 (ptm) cc_final: -0.0262 (mpm) REVERT: C 375 PHE cc_start: 0.8397 (t80) cc_final: 0.7930 (t80) REVERT: C 529 LYS cc_start: 0.8123 (mttt) cc_final: 0.7424 (tppt) REVERT: C 574 ASP cc_start: 0.7351 (p0) cc_final: 0.7076 (p0) REVERT: C 634 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8487 (mpt180) REVERT: C 731 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9101 (ptp) REVERT: C 740 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8516 (ttp) REVERT: C 1010 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8126 (mm-40) REVERT: C 1107 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7715 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8360 (t0) cc_final: 0.8008 (t0) REVERT: C 1141 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7227 (mt) outliers start: 71 outliers final: 53 residues processed: 291 average time/residue: 0.4422 time to fit residues: 157.7036 Evaluate side-chains 292 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 141 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 236 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 293 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 774 GLN C 914 ASN C1125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120647 restraints weight = 30985.168| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.97 r_work: 0.3245 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.468 26131 Z= 0.272 Angle : 0.925 59.199 35654 Z= 0.541 Chirality : 0.050 1.126 4155 Planarity : 0.004 0.101 4491 Dihedral : 5.074 54.575 4526 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 2.72 % Allowed : 15.68 % Favored : 81.60 % Cbeta Deviations : 0.07 % 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: 0.29 (0.15), residues: 3100 helix: 2.33 (0.19), residues: 720 sheet: 0.61 (0.19), residues: 653 loop : -0.95 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B1107 TYR 0.018 0.001 TYR C1067 PHE 0.027 0.001 PHE A 392 TRP 0.032 0.002 TRP C 452 HIS 0.007 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00586 (26037) covalent geometry : angle 0.88662 (35410) SS BOND : bond 0.06318 ( 38) SS BOND : angle 4.54583 ( 76) hydrogen bonds : bond 0.03991 ( 1019) hydrogen bonds : angle 5.45917 ( 2901) link_BETA1-4 : bond 0.00503 ( 21) link_BETA1-4 : angle 1.42838 ( 63) link_NAG-ASN : bond 0.00365 ( 35) link_NAG-ASN : angle 3.02479 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9288.74 seconds wall clock time: 158 minutes 55.58 seconds (9535.58 seconds total)