Starting phenix.real_space_refine on Sun Jun 22 04:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eln_48156/06_2025/9eln_48156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eln_48156/06_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_48156/06_2025/9eln_48156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eln_48156/06_2025/9eln_48156.map" model { file = "/net/cci-nas-00/data/ceres_data/9eln_48156/06_2025/9eln_48156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eln_48156/06_2025/9eln_48156.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.34, per 1000 atoms: 0.68 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: 6.79 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.23 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: 11.77 Time building geometry restraints manager: 8.11 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 1150 or resid 1301 thr \ ough 1305)) selection = (chain 'B' and (resid 26 through 138 or resid 154 through 676 or resid 689 throu \ gh 837 or resid 852 through 1150 or resid 1301 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 1150 or resid 1 \ 301 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: 9.680 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: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 63.150 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.003 TRP C 452 HIS 0.022 0.002 HIS B1048 PHE 0.064 0.003 PHE A 392 TYR 0.026 0.003 TYR B 380 ARG 0.041 0.002 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 35) link_NAG-ASN : angle 4.51643 ( 105) link_BETA1-4 : bond 0.00455 ( 21) link_BETA1-4 : angle 1.72500 ( 63) hydrogen bonds : bond 0.13450 ( 1019) hydrogen bonds : angle 7.66032 ( 2901) SS BOND : bond 0.06807 ( 38) SS BOND : angle 5.37291 ( 76) covalent geometry : bond 0.01185 (26037) covalent geometry : angle 1.36806 (35410) *********************** 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 : 2.557 Fit side-chains 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: 0.5433 (m-80) REVERT: B 192 PHE cc_start: 0.6423 (m-80) cc_final: 0.5949 (m-10) REVERT: B 568 ASP cc_start: 0.8428 (m-30) cc_final: 0.8181 (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: 0.6842 (m-10) REVERT: C 153 MET cc_start: 0.1485 (ptm) cc_final: -0.0305 (mpm) REVERT: C 237 ARG cc_start: 0.8337 (mtm180) cc_final: 0.8118 (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: 0.6086 (t0) REVERT: C 425 LEU cc_start: 0.8122 (mp) cc_final: 0.7915 (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: 0.7940 (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 1101 HIS cc_start: 0.8361 (m90) cc_final: 0.8160 (m90) 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: 1.1395 time to fit residues: 737.1286 Evaluate side-chains 299 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 265 optimal weight: 0.0170 chunk 237 optimal weight: 4.9990 chunk 132 optimal weight: 0.0570 chunk 81 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 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 B1002 GLN C 196 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137618 restraints weight = 31053.789| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.07 r_work: 0.3259 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26131 Z= 0.158 Angle : 0.708 19.240 35654 Z= 0.360 Chirality : 0.048 0.415 4155 Planarity : 0.005 0.085 4491 Dihedral : 8.405 64.172 4527 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.76 % Allowed : 12.23 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3100 helix: 2.22 (0.19), residues: 723 sheet: 1.10 (0.20), residues: 619 loop : -0.58 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 452 HIS 0.007 0.001 HIS B1083 PHE 0.031 0.002 PHE C 135 TYR 0.021 0.002 TYR C 453 ARG 0.007 0.001 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 35) link_NAG-ASN : angle 3.92557 ( 105) link_BETA1-4 : bond 0.00776 ( 21) link_BETA1-4 : angle 2.18669 ( 63) hydrogen bonds : bond 0.04854 ( 1019) hydrogen bonds : angle 6.12946 ( 2901) SS BOND : bond 0.00450 ( 38) SS BOND : angle 1.75530 ( 76) covalent geometry : bond 0.00360 (26037) covalent geometry : angle 0.66626 (35410) *********************** 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 397 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 321 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8106 (mt) cc_final: 0.7800 (tt) REVERT: A 349 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8062 (p) REVERT: A 396 TYR cc_start: 0.7900 (m-80) cc_final: 0.7469 (m-80) REVERT: A 470 THR cc_start: 0.8552 (p) cc_final: 0.8275 (t) REVERT: A 571 ASP cc_start: 0.8004 (t70) cc_final: 0.7710 (t0) REVERT: A 591 SER cc_start: 0.8753 (t) cc_final: 0.8476 (m) REVERT: A 625 HIS cc_start: 0.8046 (m-70) cc_final: 0.7712 (m-70) REVERT: A 654 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: A 740 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7682 (ttt) REVERT: B 195 LYS cc_start: 0.7430 (tmmt) cc_final: 0.7070 (tmmt) REVERT: B 202 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7227 (mttt) REVERT: B 568 ASP cc_start: 0.8517 (m-30) cc_final: 0.8216 (m-30) REVERT: B 619 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: B 775 ASP cc_start: 0.8310 (m-30) cc_final: 0.8082 (m-30) REVERT: B 790 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8568 (mmtp) REVERT: B 935 GLN cc_start: 0.8179 (tt0) cc_final: 0.7887 (tt0) REVERT: B 1101 HIS cc_start: 0.8046 (m90) cc_final: 0.7792 (m90) REVERT: C 100 ILE cc_start: 0.6453 (mp) cc_final: 0.6235 (mm) REVERT: C 153 MET cc_start: 0.1488 (ptm) cc_final: -0.0398 (mpm) REVERT: C 169 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7151 (mp0) REVERT: C 170 TYR cc_start: 0.8124 (t80) cc_final: 0.7921 (t80) REVERT: C 190 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7126 (mtt90) REVERT: C 237 ARG cc_start: 0.8349 (mtm180) cc_final: 0.7885 (mtp85) REVERT: C 338 PHE cc_start: 0.7535 (m-80) cc_final: 0.7245 (m-80) REVERT: C 375 PHE cc_start: 0.7915 (t80) cc_final: 0.7401 (t80) REVERT: C 422 ASN cc_start: 0.7473 (m110) cc_final: 0.7102 (p0) REVERT: C 529 LYS cc_start: 0.7765 (mttt) cc_final: 0.7244 (tppt) REVERT: C 618 THR cc_start: 0.8798 (m) cc_final: 0.8512 (p) REVERT: C 904 TYR cc_start: 0.7737 (t80) cc_final: 0.7430 (t80) REVERT: C 1005 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: C 1010 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7986 (mm-40) outliers start: 76 outliers final: 31 residues processed: 378 average time/residue: 0.9636 time to fit residues: 444.4731 Evaluate side-chains 293 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 3.193 ------------------------------------------------------------------------------- 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 399 SER 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 875 SER Chi-restraints excluded: chain B residue 1010 GLN 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 0 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 169 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 C 61 ASN 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 C 779 GLN C 914 ASN C1125 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123660 restraints weight = 30889.184| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.27 r_work: 0.3211 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26131 Z= 0.173 Angle : 0.649 17.311 35654 Z= 0.332 Chirality : 0.047 0.424 4155 Planarity : 0.005 0.066 4491 Dihedral : 5.951 55.271 4527 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.30 % Allowed : 12.74 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3100 helix: 2.25 (0.19), residues: 717 sheet: 0.96 (0.20), residues: 628 loop : -0.79 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 452 HIS 0.008 0.001 HIS A1101 PHE 0.033 0.002 PHE A 515 TYR 0.025 0.002 TYR C 453 ARG 0.005 0.001 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 35) link_NAG-ASN : angle 3.30926 ( 105) link_BETA1-4 : bond 0.00720 ( 21) link_BETA1-4 : angle 1.97843 ( 63) hydrogen bonds : bond 0.04733 ( 1019) hydrogen bonds : angle 5.78420 ( 2901) SS BOND : bond 0.00481 ( 38) SS BOND : angle 1.46577 ( 76) covalent geometry : bond 0.00406 (26037) covalent geometry : angle 0.61681 (35410) *********************** 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 379 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 288 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7059 (mtpt) REVERT: A 349 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8066 (p) REVERT: A 396 TYR cc_start: 0.8177 (m-80) cc_final: 0.7746 (m-80) REVERT: A 493 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: A 571 ASP cc_start: 0.8089 (t70) cc_final: 0.7742 (t0) REVERT: A 591 SER cc_start: 0.8975 (t) cc_final: 0.8698 (m) REVERT: A 625 HIS cc_start: 0.8179 (m-70) cc_final: 0.7836 (m-70) REVERT: A 654 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: A 921 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8157 (mtpm) REVERT: B 126 VAL cc_start: 0.6049 (m) cc_final: 0.5376 (p) REVERT: B 195 LYS cc_start: 0.7757 (tmmt) cc_final: 0.7415 (tmmt) REVERT: B 304 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7605 (mptt) REVERT: B 619 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: B 775 ASP cc_start: 0.8609 (m-30) cc_final: 0.8334 (m-30) REVERT: B 916 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 1101 HIS cc_start: 0.8320 (m90) cc_final: 0.7988 (m90) REVERT: B 1142 GLN cc_start: 0.7185 (tp40) cc_final: 0.6657 (tm-30) REVERT: C 153 MET cc_start: 0.1518 (ptm) cc_final: -0.0415 (mpm) REVERT: C 169 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7446 (mp0) REVERT: C 190 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7332 (mtt90) REVERT: C 375 PHE cc_start: 0.8120 (t80) cc_final: 0.7624 (t80) REVERT: C 460 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7094 (tptm) REVERT: C 529 LYS cc_start: 0.7987 (mttt) cc_final: 0.7396 (tppt) REVERT: C 904 TYR cc_start: 0.8037 (t80) cc_final: 0.7648 (t80) REVERT: C 1010 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8108 (mm-40) REVERT: C 1107 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7699 (mtp-110) REVERT: C 1141 LEU cc_start: 0.7780 (tp) cc_final: 0.7307 (mt) outliers start: 91 outliers final: 40 residues processed: 353 average time/residue: 1.2497 time to fit residues: 532.2919 Evaluate side-chains 301 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 87 ASN 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 441 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 503 VAL 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 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 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 208 THR 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 645 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 193 optimal weight: 0.2980 chunk 293 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 238 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 278 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 505 HIS A 540 ASN A 960 ASN B 61 ASN B 134 GLN B 703 ASN B 954 HIS C 239 GLN C 280 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 774 GLN C 779 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124157 restraints weight = 31180.880| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.13 r_work: 0.3234 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26131 Z= 0.125 Angle : 0.595 16.049 35654 Z= 0.302 Chirality : 0.045 0.381 4155 Planarity : 0.004 0.056 4491 Dihedral : 5.262 53.607 4526 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.01 % Allowed : 13.58 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3100 helix: 2.37 (0.19), residues: 714 sheet: 0.84 (0.19), residues: 646 loop : -0.82 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 452 HIS 0.008 0.001 HIS B 954 PHE 0.026 0.001 PHE A 392 TYR 0.024 0.001 TYR A 170 ARG 0.007 0.000 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 35) link_NAG-ASN : angle 3.27049 ( 105) link_BETA1-4 : bond 0.00597 ( 21) link_BETA1-4 : angle 1.77820 ( 63) hydrogen bonds : bond 0.04143 ( 1019) hydrogen bonds : angle 5.63484 ( 2901) SS BOND : bond 0.00552 ( 38) SS BOND : angle 1.69329 ( 76) covalent geometry : bond 0.00283 (26037) covalent geometry : angle 0.55986 (35410) *********************** 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 348 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 265 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7035 (mttm) REVERT: A 349 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 498 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6755 (mtp85) REVERT: A 571 ASP cc_start: 0.8048 (t70) cc_final: 0.7679 (t0) REVERT: A 591 SER cc_start: 0.8940 (t) cc_final: 0.8664 (m) REVERT: A 625 HIS cc_start: 0.8126 (m-70) cc_final: 0.7774 (m-70) REVERT: A 654 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 740 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7848 (tmt) REVERT: B 168 PHE cc_start: 0.5795 (m-80) cc_final: 0.5347 (m-80) REVERT: B 239 GLN cc_start: 0.7367 (tp40) cc_final: 0.6933 (tp40) REVERT: B 304 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7615 (mptt) REVERT: B 619 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: B 745 ASP cc_start: 0.6773 (p0) cc_final: 0.6508 (p0) REVERT: B 759 PHE cc_start: 0.7857 (t80) cc_final: 0.7260 (m-80) REVERT: B 775 ASP cc_start: 0.8452 (m-30) cc_final: 0.8185 (m-30) REVERT: B 916 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 1101 HIS cc_start: 0.8287 (m90) cc_final: 0.8041 (m90) REVERT: B 1142 GLN cc_start: 0.7200 (tp40) cc_final: 0.6709 (tm-30) REVERT: C 153 MET cc_start: 0.1546 (ptm) cc_final: -0.0320 (mpm) REVERT: C 190 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7437 (mtt90) REVERT: C 375 PHE cc_start: 0.8158 (t80) cc_final: 0.7661 (t80) REVERT: C 460 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7166 (tptm) REVERT: C 529 LYS cc_start: 0.7945 (mttt) cc_final: 0.7392 (tppt) REVERT: C 628 GLN cc_start: 0.7962 (mm110) cc_final: 0.7397 (pt0) REVERT: C 634 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8441 (mpt180) REVERT: C 731 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9041 (ptp) REVERT: C 904 TYR cc_start: 0.8007 (t80) cc_final: 0.7685 (t80) REVERT: C 1010 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8125 (mm-40) REVERT: C 1107 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7725 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8474 (t0) cc_final: 0.8196 (t0) outliers start: 83 outliers final: 39 residues processed: 325 average time/residue: 1.5427 time to fit residues: 612.0584 Evaluate side-chains 294 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 9.119 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 590 CYS 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 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 164 ASN 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 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 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1010 GLN 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 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 205 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 272 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 285 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 703 ASN C 280 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 703 ASN C 774 GLN C 779 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118945 restraints weight = 31059.632| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.03 r_work: 0.3206 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26131 Z= 0.181 Angle : 0.619 15.804 35654 Z= 0.315 Chirality : 0.046 0.422 4155 Planarity : 0.004 0.055 4491 Dihedral : 5.240 56.613 4526 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.45 % Allowed : 13.76 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3100 helix: 2.31 (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 TRP 0.029 0.002 TRP A 452 HIS 0.010 0.001 HIS A1101 PHE 0.040 0.002 PHE A 392 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 35) link_NAG-ASN : angle 3.17247 ( 105) link_BETA1-4 : bond 0.00592 ( 21) link_BETA1-4 : angle 1.63678 ( 63) hydrogen bonds : bond 0.04526 ( 1019) hydrogen bonds : angle 5.66430 ( 2901) SS BOND : bond 0.00556 ( 38) SS BOND : angle 1.71540 ( 76) covalent geometry : bond 0.00431 (26037) covalent geometry : angle 0.58681 (35410) *********************** 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 339 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 244 time to evaluate : 2.579 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: 0.7163 (mttp) REVERT: A 349 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 440 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8132 (mmpt) REVERT: A 493 GLN cc_start: 0.7522 (tt0) cc_final: 0.6968 (tp40) REVERT: A 571 ASP cc_start: 0.8085 (t70) cc_final: 0.7641 (t0) REVERT: A 591 SER cc_start: 0.8936 (t) cc_final: 0.8677 (m) REVERT: A 625 HIS cc_start: 0.8101 (m-70) cc_final: 0.7700 (m-70) REVERT: A 654 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: B 126 VAL cc_start: 0.6225 (m) cc_final: 0.5565 (p) REVERT: B 164 ASN cc_start: 0.5805 (m-40) cc_final: 0.5347 (t0) REVERT: B 168 PHE cc_start: 0.5806 (m-80) cc_final: 0.5434 (m-80) REVERT: B 195 LYS cc_start: 0.7954 (tmmt) cc_final: 0.7661 (tmmt) REVERT: B 304 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7529 (mptt) REVERT: B 619 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: B 745 ASP cc_start: 0.6930 (p0) cc_final: 0.6675 (p0) REVERT: B 759 PHE cc_start: 0.7898 (t80) cc_final: 0.7239 (m-80) REVERT: B 775 ASP cc_start: 0.8597 (m-30) cc_final: 0.8364 (m-30) REVERT: B 916 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 1101 HIS cc_start: 0.8312 (m90) cc_final: 0.7979 (m90) REVERT: B 1142 GLN cc_start: 0.7167 (tp40) cc_final: 0.6636 (tm-30) REVERT: C 153 MET cc_start: 0.1522 (ptm) cc_final: -0.0203 (mpm) REVERT: C 190 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7360 (mtt90) REVERT: C 375 PHE cc_start: 0.8351 (t80) cc_final: 0.7898 (t80) REVERT: C 460 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7230 (tptm) REVERT: C 529 LYS cc_start: 0.8063 (mttt) cc_final: 0.7396 (tppt) REVERT: C 628 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7333 (pt0) REVERT: C 731 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9060 (ptp) REVERT: C 904 TYR cc_start: 0.7955 (t80) cc_final: 0.7624 (t80) REVERT: C 918 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: C 1010 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8090 (mm-40) REVERT: C 1107 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7728 (mtp-110) outliers start: 95 outliers final: 47 residues processed: 317 average time/residue: 1.0475 time to fit residues: 400.4765 Evaluate side-chains 287 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS 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 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 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 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 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 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU 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 208 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 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 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.0070 chunk 245 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 A1119 ASN B 26 GLN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS C 703 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 = 0.3997 r_free = 0.3997 target = 0.175079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131646 restraints weight = 30775.792| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.24 r_work: 0.3151 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26131 Z= 0.141 Angle : 0.591 14.852 35654 Z= 0.299 Chirality : 0.045 0.389 4155 Planarity : 0.004 0.053 4491 Dihedral : 5.123 54.797 4526 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.09 % Allowed : 14.45 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3100 helix: 2.35 (0.19), residues: 713 sheet: 0.66 (0.20), residues: 639 loop : -0.94 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 452 HIS 0.007 0.001 HIS A1101 PHE 0.027 0.001 PHE A 392 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 35) link_NAG-ASN : angle 2.99600 ( 105) link_BETA1-4 : bond 0.00555 ( 21) link_BETA1-4 : angle 1.52413 ( 63) hydrogen bonds : bond 0.04188 ( 1019) hydrogen bonds : angle 5.58535 ( 2901) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.66122 ( 76) covalent geometry : bond 0.00330 (26037) covalent geometry : angle 0.56135 (35410) *********************** 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 335 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 250 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7091 (mmtm) REVERT: A 314 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: A 349 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 440 LYS cc_start: 0.8424 (mmpt) cc_final: 0.8182 (mmpt) REVERT: A 493 GLN cc_start: 0.7489 (tt0) cc_final: 0.7013 (tp40) REVERT: A 571 ASP cc_start: 0.8061 (t70) cc_final: 0.7643 (t0) REVERT: A 591 SER cc_start: 0.8911 (t) cc_final: 0.8669 (m) REVERT: A 625 HIS cc_start: 0.8028 (m-70) cc_final: 0.7696 (m-70) REVERT: A 654 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: A 1045 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: B 164 ASN cc_start: 0.5805 (m-40) cc_final: 0.5296 (t0) REVERT: B 168 PHE cc_start: 0.5882 (m-80) cc_final: 0.5545 (m-80) REVERT: B 239 GLN cc_start: 0.7376 (tp40) cc_final: 0.6826 (mm110) REVERT: B 304 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7572 (mptt) REVERT: B 619 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: B 745 ASP cc_start: 0.6974 (p0) cc_final: 0.6674 (p0) REVERT: B 775 ASP cc_start: 0.8421 (m-30) cc_final: 0.8207 (m-30) REVERT: B 916 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 1101 HIS cc_start: 0.8236 (m90) cc_final: 0.8018 (m90) REVERT: B 1142 GLN cc_start: 0.7235 (tp40) cc_final: 0.6735 (tm-30) REVERT: C 153 MET cc_start: 0.1538 (ptm) cc_final: -0.0161 (mpm) REVERT: C 190 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7463 (mtt90) REVERT: C 375 PHE cc_start: 0.8334 (t80) cc_final: 0.7837 (t80) REVERT: C 460 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7602 (mmtm) REVERT: C 529 LYS cc_start: 0.8047 (mttt) cc_final: 0.7456 (tppt) REVERT: C 628 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7419 (pt0) REVERT: C 731 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.9010 (ptp) REVERT: C 904 TYR cc_start: 0.7851 (t80) cc_final: 0.7613 (t80) REVERT: C 914 ASN cc_start: 0.7929 (t0) cc_final: 0.7715 (t0) REVERT: C 1010 GLN cc_start: 0.8232 (mm-40) cc_final: 0.8003 (mm-40) outliers start: 85 outliers final: 44 residues processed: 317 average time/residue: 1.2867 time to fit residues: 501.1088 Evaluate side-chains 282 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 3.648 ------------------------------------------------------------------------------- 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 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS 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 676 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1045 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 193 VAL Chi-restraints excluded: chain B residue 240 THR 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 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU 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 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 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 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 22 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 A1119 ASN B 61 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 703 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.172984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118738 restraints weight = 30908.225| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.03 r_work: 0.3192 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26131 Z= 0.194 Angle : 0.626 14.787 35654 Z= 0.317 Chirality : 0.047 0.425 4155 Planarity : 0.004 0.054 4491 Dihedral : 5.267 57.152 4526 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 14.63 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3100 helix: 2.27 (0.19), residues: 713 sheet: 0.59 (0.20), residues: 622 loop : -0.98 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 452 HIS 0.006 0.001 HIS A1101 PHE 0.030 0.002 PHE A 392 TYR 0.018 0.001 TYR B1067 ARG 0.012 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 35) link_NAG-ASN : angle 3.02941 ( 105) link_BETA1-4 : bond 0.00556 ( 21) link_BETA1-4 : angle 1.50185 ( 63) hydrogen bonds : bond 0.04564 ( 1019) hydrogen bonds : angle 5.66311 ( 2901) SS BOND : bond 0.00656 ( 38) SS BOND : angle 1.73457 ( 76) covalent geometry : bond 0.00466 (26037) covalent geometry : angle 0.59739 (35410) *********************** 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 318 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 233 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7035 (mmtm) REVERT: A 309 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: A 349 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 493 GLN cc_start: 0.7569 (tt0) cc_final: 0.7051 (tp40) REVERT: A 571 ASP cc_start: 0.8099 (t70) cc_final: 0.7683 (t0) REVERT: A 591 SER cc_start: 0.8957 (t) cc_final: 0.8698 (m) REVERT: A 654 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: B 126 VAL cc_start: 0.6298 (m) cc_final: 0.5631 (p) REVERT: B 164 ASN cc_start: 0.5713 (m-40) cc_final: 0.5017 (t0) REVERT: B 168 PHE cc_start: 0.5908 (m-80) cc_final: 0.5556 (m-80) REVERT: B 195 LYS cc_start: 0.8087 (tmmt) cc_final: 0.7644 (tmmt) REVERT: B 304 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7569 (mptt) REVERT: B 619 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: B 775 ASP cc_start: 0.8598 (m-30) cc_final: 0.8363 (m-30) REVERT: B 916 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 1101 HIS cc_start: 0.8361 (m90) cc_final: 0.8026 (m90) REVERT: C 32 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7123 (t80) REVERT: C 153 MET cc_start: 0.1582 (ptm) cc_final: -0.0265 (mpm) REVERT: C 190 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7429 (mtt90) REVERT: C 375 PHE cc_start: 0.8381 (t80) cc_final: 0.7908 (t80) REVERT: C 460 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7569 (mmtm) REVERT: C 529 LYS cc_start: 0.8145 (mttt) cc_final: 0.7512 (tppt) REVERT: C 628 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7380 (pt0) REVERT: C 731 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9035 (ptp) REVERT: C 904 TYR cc_start: 0.7945 (t80) cc_final: 0.7628 (t80) REVERT: C 1010 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8113 (mm-40) outliers start: 85 outliers final: 51 residues processed: 299 average time/residue: 1.0645 time to fit residues: 384.0744 Evaluate side-chains 283 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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 129 LYS Chi-restraints excluded: chain A residue 309 GLU 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 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS 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 676 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 888 PHE 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 193 VAL Chi-restraints excluded: chain B residue 240 THR 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 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 208 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 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 859 THR 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 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 305 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 263 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 321 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 954 HIS C 774 GLN C1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120581 restraints weight = 30869.803| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.02 r_work: 0.3230 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26131 Z= 0.126 Angle : 0.580 13.739 35654 Z= 0.294 Chirality : 0.045 0.372 4155 Planarity : 0.004 0.054 4491 Dihedral : 5.178 53.872 4526 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 15.72 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3100 helix: 2.34 (0.19), residues: 720 sheet: 0.59 (0.20), residues: 634 loop : -0.97 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 452 HIS 0.007 0.001 HIS B 954 PHE 0.029 0.001 PHE C 490 TYR 0.019 0.001 TYR C 453 ARG 0.009 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 35) link_NAG-ASN : angle 2.95061 ( 105) link_BETA1-4 : bond 0.00539 ( 21) link_BETA1-4 : angle 1.40407 ( 63) hydrogen bonds : bond 0.03987 ( 1019) hydrogen bonds : angle 5.51715 ( 2901) SS BOND : bond 0.00398 ( 38) SS BOND : angle 1.45763 ( 76) covalent geometry : bond 0.00287 (26037) covalent geometry : angle 0.55213 (35410) *********************** 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 311 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 246 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6987 (mmtm) REVERT: A 349 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 493 GLN cc_start: 0.7499 (tt0) cc_final: 0.7016 (tp40) REVERT: A 571 ASP cc_start: 0.8082 (t70) cc_final: 0.7706 (t0) REVERT: A 591 SER cc_start: 0.8968 (t) cc_final: 0.8707 (m) REVERT: A 641 ASN cc_start: 0.8278 (t0) cc_final: 0.8070 (t0) REVERT: A 654 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 791 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 164 ASN cc_start: 0.5557 (m-40) cc_final: 0.4905 (t0) REVERT: B 168 PHE cc_start: 0.5900 (m-80) cc_final: 0.5510 (m-80) REVERT: B 237 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: B 304 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7521 (mptt) REVERT: B 619 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 775 ASP cc_start: 0.8461 (m-30) cc_final: 0.8246 (m-30) REVERT: B 916 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 1101 HIS cc_start: 0.8365 (m90) cc_final: 0.8021 (m90) REVERT: C 32 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 153 MET cc_start: 0.1611 (ptm) cc_final: -0.0247 (mpm) REVERT: C 190 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7529 (mtt90) REVERT: C 375 PHE cc_start: 0.8413 (t80) cc_final: 0.7957 (t80) REVERT: C 460 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7600 (mmtm) REVERT: C 529 LYS cc_start: 0.8120 (mttt) cc_final: 0.7496 (tppt) REVERT: C 628 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7351 (pt0) REVERT: C 731 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9076 (ptp) REVERT: C 904 TYR cc_start: 0.7911 (t80) cc_final: 0.7610 (t80) REVERT: C 1010 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8090 (mm-40) REVERT: C 1139 ASP cc_start: 0.8358 (t0) cc_final: 0.8011 (t0) outliers start: 65 outliers final: 40 residues processed: 297 average time/residue: 1.0845 time to fit residues: 392.0962 Evaluate side-chains 277 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 129 LYS Chi-restraints excluded: chain A residue 312 ILE 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 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 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 888 PHE Chi-restraints excluded: chain A residue 1045 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 108 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 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 723 THR 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 208 THR Chi-restraints excluded: chain C residue 356 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 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 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 268 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 291 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 954 HIS C 280 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121487 restraints weight = 31087.951| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3218 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26131 Z= 0.135 Angle : 0.592 13.555 35654 Z= 0.298 Chirality : 0.045 0.385 4155 Planarity : 0.004 0.053 4491 Dihedral : 5.129 55.336 4526 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.65 % Allowed : 15.64 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3100 helix: 2.35 (0.19), residues: 721 sheet: 0.58 (0.20), residues: 631 loop : -0.95 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 452 HIS 0.010 0.001 HIS B 954 PHE 0.026 0.001 PHE A 392 TYR 0.020 0.001 TYR C 453 ARG 0.012 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 35) link_NAG-ASN : angle 2.80594 ( 105) link_BETA1-4 : bond 0.00528 ( 21) link_BETA1-4 : angle 1.39011 ( 63) hydrogen bonds : bond 0.04074 ( 1019) hydrogen bonds : angle 5.49956 ( 2901) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.52783 ( 76) covalent geometry : bond 0.00316 (26037) covalent geometry : angle 0.56700 (35410) *********************** 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 306 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 233 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7000 (mmtm) REVERT: A 349 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 493 GLN cc_start: 0.7490 (tt0) cc_final: 0.6997 (tp40) REVERT: A 571 ASP cc_start: 0.8114 (t70) cc_final: 0.7717 (t0) REVERT: A 591 SER cc_start: 0.8994 (t) cc_final: 0.8749 (m) REVERT: A 625 HIS cc_start: 0.7965 (m90) cc_final: 0.7744 (m90) REVERT: A 641 ASN cc_start: 0.8280 (t0) cc_final: 0.8027 (t160) REVERT: A 654 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 164 ASN cc_start: 0.5579 (m-40) cc_final: 0.4911 (t0) REVERT: B 168 PHE cc_start: 0.5929 (m-80) cc_final: 0.5515 (m-80) REVERT: B 237 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: B 304 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7546 (mptt) REVERT: B 619 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 775 ASP cc_start: 0.8496 (m-30) cc_final: 0.8273 (m-30) REVERT: B 916 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (tt) REVERT: B 1101 HIS cc_start: 0.8388 (m90) cc_final: 0.8020 (m90) REVERT: C 32 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7125 (t80) REVERT: C 153 MET cc_start: 0.1583 (ptm) cc_final: -0.0270 (mpm) REVERT: C 190 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7555 (mtt90) REVERT: C 375 PHE cc_start: 0.8392 (t80) cc_final: 0.7959 (t80) REVERT: C 460 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7620 (mmtm) REVERT: C 529 LYS cc_start: 0.8128 (mttt) cc_final: 0.7503 (tppt) REVERT: C 628 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7337 (pt0) REVERT: C 904 TYR cc_start: 0.7956 (t80) cc_final: 0.7639 (t80) REVERT: C 1010 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8105 (mm-40) REVERT: C 1107 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7715 (mtp-110) REVERT: C 1139 ASP cc_start: 0.8346 (t0) cc_final: 0.8015 (t0) outliers start: 73 outliers final: 42 residues processed: 289 average time/residue: 1.0508 time to fit residues: 368.5285 Evaluate side-chains 277 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 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 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 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 888 PHE 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 193 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 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 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE 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 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 859 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 1 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 276 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 321 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118710 restraints weight = 31028.588| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.00 r_work: 0.3202 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26131 Z= 0.172 Angle : 0.618 13.955 35654 Z= 0.313 Chirality : 0.046 0.403 4155 Planarity : 0.004 0.053 4491 Dihedral : 5.263 56.271 4526 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.25 % Allowed : 16.15 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3100 helix: 2.25 (0.19), residues: 721 sheet: 0.45 (0.20), residues: 645 loop : -1.01 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 452 HIS 0.004 0.001 HIS A1101 PHE 0.027 0.002 PHE A 392 TYR 0.018 0.001 TYR C1067 ARG 0.011 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 35) link_NAG-ASN : angle 3.08569 ( 105) link_BETA1-4 : bond 0.00522 ( 21) link_BETA1-4 : angle 1.36471 ( 63) hydrogen bonds : bond 0.04328 ( 1019) hydrogen bonds : angle 5.59905 ( 2901) SS BOND : bond 0.00442 ( 38) SS BOND : angle 1.86055 ( 76) covalent geometry : bond 0.00413 (26037) covalent geometry : angle 0.58792 (35410) ********************** 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 283 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6827 (mmtm) REVERT: A 309 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: A 347 PHE cc_start: 0.6164 (m-10) cc_final: 0.5937 (m-10) REVERT: A 349 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.8118 (p) REVERT: A 378 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7684 (mttm) REVERT: A 493 GLN cc_start: 0.7487 (tt0) cc_final: 0.6989 (tp40) REVERT: A 571 ASP cc_start: 0.8022 (t70) cc_final: 0.7628 (t0) REVERT: A 591 SER cc_start: 0.8978 (t) cc_final: 0.8731 (m) REVERT: A 641 ASN cc_start: 0.8277 (t0) cc_final: 0.8004 (t160) REVERT: A 654 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 164 ASN cc_start: 0.5614 (m-40) cc_final: 0.4891 (t0) REVERT: B 168 PHE cc_start: 0.6018 (m-80) cc_final: 0.5598 (m-80) REVERT: B 239 GLN cc_start: 0.7364 (tt0) cc_final: 0.7010 (mm110) REVERT: B 304 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7582 (mptt) REVERT: B 619 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 775 ASP cc_start: 0.8547 (m-30) cc_final: 0.8319 (m-30) REVERT: B 916 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 1101 HIS cc_start: 0.8393 (m90) cc_final: 0.8030 (m90) REVERT: C 153 MET cc_start: 0.1681 (ptm) cc_final: -0.0182 (mpm) REVERT: C 190 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7562 (mtt90) REVERT: C 202 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (mttp) REVERT: C 375 PHE cc_start: 0.8438 (t80) cc_final: 0.8058 (t80) REVERT: C 460 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7602 (mmtm) REVERT: C 529 LYS cc_start: 0.8150 (mttt) cc_final: 0.7509 (tppt) REVERT: C 628 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7334 (pt0) REVERT: C 904 TYR cc_start: 0.7921 (t80) cc_final: 0.7609 (t80) REVERT: C 1010 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8119 (mm-40) outliers start: 62 outliers final: 43 residues processed: 272 average time/residue: 0.9764 time to fit residues: 323.7332 Evaluate side-chains 269 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 2.683 ------------------------------------------------------------------------------- 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 309 GLU 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 378 LYS 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 608 VAL Chi-restraints excluded: chain A residue 620 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 888 PHE 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 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE 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 916 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 356 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 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 859 THR 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 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 307 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 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** B 954 HIS C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122194 restraints weight = 30902.216| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.17 r_work: 0.3203 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 26131 Z= 0.146 Angle : 0.721 48.011 35654 Z= 0.384 Chirality : 0.046 0.386 4155 Planarity : 0.004 0.051 4491 Dihedral : 5.209 55.314 4526 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 2.18 % Allowed : 16.30 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3100 helix: 2.28 (0.19), residues: 721 sheet: 0.44 (0.20), residues: 637 loop : -0.99 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 452 HIS 0.012 0.001 HIS B 954 PHE 0.042 0.001 PHE B 392 TYR 0.018 0.001 TYR C1067 ARG 0.012 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 35) link_NAG-ASN : angle 3.08600 ( 105) link_BETA1-4 : bond 0.00517 ( 21) link_BETA1-4 : angle 1.34304 ( 63) hydrogen bonds : bond 0.04174 ( 1019) hydrogen bonds : angle 5.57097 ( 2901) SS BOND : bond 0.00442 ( 38) SS BOND : angle 1.65831 ( 76) covalent geometry : bond 0.00351 (26037) covalent geometry : angle 0.69684 (35410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20531.84 seconds wall clock time: 359 minutes 26.27 seconds (21566.27 seconds total)