Starting phenix.real_space_refine on Fri Sep 19 12:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.map" model { file = "/net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elj_48151/09_2025/9elj_48151.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 16314 2.51 5 N 4157 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25558 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8281 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 56, 'TRANS': 998} Chain breaks: 6 Chain: "B" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8234 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8266 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.56, per 1000 atoms: 0.26 Number of scatterers: 25558 At special positions: 0 Unit cell: (132.83, 137.138, 198.886, 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 4976 8.00 N 4157 7.00 C 16314 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.04 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=2, 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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 B 30 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 234 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " 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 B 709 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5914 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 41 sheets defined 26.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 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: 3.568A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.521A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.662A 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 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: 4.506A 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 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.634A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (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: 3.762A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.376A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.584A 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 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.069A 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 498 through 502 removed outlier: 3.554A pdb=" N TYR B 501 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 498 through 502' 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 removed outlier: 4.019A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.572A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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: 4.140A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.631A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.810A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.722A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 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 removed outlier: 3.592A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 888 No H-bonds generated for 'chain 'C' and resid 886 through 888' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.674A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.691A 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 removed outlier: 3.788A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1150 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.100A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.915A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.603A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.198A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.543A 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: 5.676A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.420A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.039A 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: 6.239A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.615A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.281A 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: 6.831A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.831A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.027A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 4.078A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 94 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.749A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 200 through 205 removed outlier: 5.438A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.314A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.503A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.337A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.546A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.546A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.537A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.872A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.726A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 63 through 65 removed outlier: 4.203A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.903A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.166A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.180A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.916A pdb=" N PHE C 392 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR C 523 " --> pdb=" O PHE C 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.611A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 1014 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7863 1.34 - 1.47: 6957 1.47 - 1.60: 11199 1.60 - 1.73: 1 1.73 - 1.86: 137 Bond restraints: 26157 Sorted by residual: bond pdb=" CA PHE B 888 " pdb=" C PHE B 888 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" CG LEU B1049 " pdb=" CD1 LEU B1049 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.04e+00 bond pdb=" N PHE B 888 " pdb=" CA PHE B 888 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.52e+00 ... (remaining 26152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 34022 2.46 - 4.91: 1357 4.91 - 7.37: 169 7.37 - 9.82: 20 9.82 - 12.28: 7 Bond angle restraints: 35575 Sorted by residual: angle pdb=" CA PRO C 463 " pdb=" N PRO C 463 " pdb=" CD PRO C 463 " ideal model delta sigma weight residual 112.00 101.71 10.29 1.40e+00 5.10e-01 5.41e+01 angle pdb=" CA PHE B 888 " pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 113.80 120.77 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " pdb=" CG ASN B 30 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" C PHE B 888 " pdb=" N GLY B 889 " pdb=" CA GLY B 889 " ideal model delta sigma weight residual 119.98 113.11 6.87 1.11e+00 8.12e-01 3.83e+01 angle pdb=" N GLY A 485 " pdb=" CA GLY A 485 " pdb=" C GLY A 485 " ideal model delta sigma weight residual 112.34 122.71 -10.37 2.04e+00 2.40e-01 2.58e+01 ... (remaining 35570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 15276 21.42 - 42.83: 726 42.83 - 64.25: 175 64.25 - 85.66: 82 85.66 - 107.08: 35 Dihedral angle restraints: 16294 sinusoidal: 7099 harmonic: 9195 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 165.81 -72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " pdb=" NH1 ARG B 357 " ideal model delta sinusoidal sigma weight residual 0.00 58.84 -58.84 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " pdb=" CZ ARG B 355 " pdb=" NH1 ARG B 355 " ideal model delta sinusoidal sigma weight residual 0.00 -47.42 47.42 1 1.00e+01 1.00e-02 3.10e+01 ... (remaining 16291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4136 0.199 - 0.399: 29 0.399 - 0.598: 0 0.598 - 0.797: 1 0.797 - 0.996: 2 Chirality restraints: 4168 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 30 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 4165 not shown) Planarity restraints: 4550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 357 " -0.777 9.50e-02 1.11e+02 3.49e-01 8.48e+01 pdb=" NE ARG B 357 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 357 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG B 357 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B 357 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 355 " -0.639 9.50e-02 1.11e+02 2.88e-01 6.14e+01 pdb=" NE ARG B 355 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 355 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 355 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG B 355 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 808 " -0.084 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO C 809 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 809 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 809 " -0.067 5.00e-02 4.00e+02 ... (remaining 4547 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 6 2.18 - 2.86: 8799 2.86 - 3.54: 34374 3.54 - 4.22: 59659 4.22 - 4.90: 102199 Nonbonded interactions: 205037 Sorted by model distance: nonbonded pdb=" CE2 TYR A 28 " pdb=" CD2 PHE A 32 " model vdw 1.501 3.640 nonbonded pdb=" O ASN C 61 " pdb=" OD1 ASN C 61 " model vdw 1.916 3.040 nonbonded pdb=" O TYR C 451 " pdb=" CD1 TRP C 452 " model vdw 1.953 3.260 nonbonded pdb=" CE2 TYR A 28 " pdb=" CE2 PHE A 32 " model vdw 2.127 3.640 nonbonded pdb=" CD2 TYR A 28 " pdb=" CE2 PHE A 32 " model vdw 2.147 3.640 ... (remaining 205032 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 73 through 138 or resid 154 through \ 172 or resid 188 through 209 or resid 213 through 388 or resid 391 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 676 or resid 689 through 837 or resid 852 through 1305)) selection = (chain 'B' and (resid 26 through 138 or resid 154 through 676 or resid 689 throu \ gh 837 or resid 852 through 1305)) selection = (chain 'C' and (resid 26 through 65 or resid 73 through 138 or resid 154 through \ 172 or resid 188 through 209 or resid 213 through 388 or resid 391 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'M' 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: 13.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.007 0.327 26254 Z= 0.386 Angle : 1.112 16.985 35822 Z= 0.612 Chirality : 0.065 0.996 4168 Planarity : 0.010 0.349 4514 Dihedral : 14.940 107.081 10266 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.14), residues: 3115 helix: 1.49 (0.18), residues: 706 sheet: 0.83 (0.21), residues: 573 loop : -0.13 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.002 ARG B 355 TYR 0.033 0.003 TYR A 612 PHE 0.056 0.003 PHE A 392 TRP 0.031 0.003 TRP A 452 HIS 0.020 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00645 (26157) covalent geometry : angle 1.08833 (35575) SS BOND : bond 0.00571 ( 38) SS BOND : angle 2.60594 ( 76) hydrogen bonds : bond 0.12148 ( 985) hydrogen bonds : angle 7.55842 ( 2853) Misc. bond : bond 0.28601 ( 2) link_BETA1-4 : bond 0.00498 ( 21) link_BETA1-4 : angle 1.62577 ( 63) link_NAG-ASN : bond 0.00781 ( 36) link_NAG-ASN : angle 3.66237 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.7181 (mt) cc_final: 0.6873 (mp) REVERT: A 190 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7380 (mtt180) REVERT: B 206 LYS cc_start: 0.7314 (tptt) cc_final: 0.7065 (tptp) REVERT: B 527 PRO cc_start: 0.8413 (Cg_exo) cc_final: 0.8063 (Cg_endo) REVERT: C 128 ILE cc_start: 0.6553 (mt) cc_final: 0.6302 (mt) REVERT: C 190 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.6801 (mtt-85) REVERT: C 380 TYR cc_start: 0.7873 (m-80) cc_final: 0.7634 (m-80) REVERT: C 464 PHE cc_start: 0.6999 (m-80) cc_final: 0.6674 (m-80) REVERT: C 1101 HIS cc_start: 0.7740 (m90) cc_final: 0.7018 (m90) outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 0.5269 time to fit residues: 173.4888 Evaluate side-chains 223 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 627 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 321 GLN A 339 HIS A 394 ASN A 505 HIS A 784 GLN A1101 HIS A1119 ASN ** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 405 ASN B 506 GLN B 913 GLN B1002 GLN B1048 HIS C 61 ASN C 804 GLN C 907 ASN C1002 GLN C1048 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.185251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135515 restraints weight = 31483.060| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.89 r_work: 0.3475 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26254 Z= 0.169 Angle : 0.692 14.478 35822 Z= 0.355 Chirality : 0.049 0.554 4168 Planarity : 0.005 0.074 4514 Dihedral : 8.398 112.419 4565 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 9.94 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.14), residues: 3115 helix: 2.18 (0.19), residues: 731 sheet: 0.59 (0.20), residues: 599 loop : -0.33 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 319 TYR 0.025 0.002 TYR A 612 PHE 0.024 0.002 PHE A 32 TRP 0.017 0.002 TRP A 452 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00388 (26157) covalent geometry : angle 0.66371 (35575) SS BOND : bond 0.00516 ( 38) SS BOND : angle 1.70847 ( 76) hydrogen bonds : bond 0.04948 ( 985) hydrogen bonds : angle 6.03278 ( 2853) Misc. bond : bond 0.00168 ( 2) link_BETA1-4 : bond 0.00665 ( 21) link_BETA1-4 : angle 2.25366 ( 63) link_NAG-ASN : bond 0.00598 ( 36) link_NAG-ASN : angle 2.97754 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7006 (mtpt) REVERT: A 351 TYR cc_start: 0.8318 (p90) cc_final: 0.8110 (p90) REVERT: A 468 ILE cc_start: 0.8433 (tp) cc_final: 0.8225 (mt) REVERT: B 206 LYS cc_start: 0.7463 (tptt) cc_final: 0.7226 (tptp) REVERT: B 1038 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8533 (ttmm) REVERT: C 83 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7876 (t) REVERT: C 190 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6684 (mtt-85) REVERT: C 281 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: C 345 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8037 (p) REVERT: C 464 PHE cc_start: 0.7010 (m-80) cc_final: 0.6675 (m-80) REVERT: C 509 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6329 (mtt-85) REVERT: C 574 ASP cc_start: 0.7793 (t0) cc_final: 0.7563 (t0) REVERT: C 584 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7479 (mt) REVERT: C 904 TYR cc_start: 0.8064 (t80) cc_final: 0.7765 (t80) REVERT: C 1101 HIS cc_start: 0.7807 (m90) cc_final: 0.7195 (m90) outliers start: 65 outliers final: 20 residues processed: 298 average time/residue: 0.4898 time to fit residues: 177.5440 Evaluate side-chains 241 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 77 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 505 HIS A1119 ASN ** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1101 HIS B1119 ASN C 61 ASN C 314 GLN C1002 GLN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128675 restraints weight = 31558.152| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.85 r_work: 0.3340 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26254 Z= 0.239 Angle : 0.699 19.883 35822 Z= 0.357 Chirality : 0.050 0.487 4168 Planarity : 0.005 0.055 4514 Dihedral : 6.444 59.783 4563 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.89 % Allowed : 10.63 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3115 helix: 2.02 (0.19), residues: 728 sheet: 0.33 (0.19), residues: 645 loop : -0.49 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 454 TYR 0.027 0.002 TYR B 170 PHE 0.035 0.002 PHE A 318 TRP 0.017 0.002 TRP B 886 HIS 0.036 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00575 (26157) covalent geometry : angle 0.67208 (35575) SS BOND : bond 0.00852 ( 38) SS BOND : angle 1.93066 ( 76) hydrogen bonds : bond 0.05281 ( 985) hydrogen bonds : angle 5.91262 ( 2853) Misc. bond : bond 0.00179 ( 2) link_BETA1-4 : bond 0.00623 ( 21) link_BETA1-4 : angle 2.07165 ( 63) link_NAG-ASN : bond 0.00529 ( 36) link_NAG-ASN : angle 2.86978 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 242 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7094 (mtpt) REVERT: A 868 GLU cc_start: 0.8257 (mp0) cc_final: 0.8001 (mt-10) REVERT: A 1002 GLN cc_start: 0.8735 (tp40) cc_final: 0.8198 (tt0) REVERT: A 1010 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: B 206 LYS cc_start: 0.7524 (tptt) cc_final: 0.7200 (tptp) REVERT: B 589 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8646 (Cg_endo) REVERT: B 627 ASP cc_start: 0.8005 (m-30) cc_final: 0.7566 (t0) REVERT: B 1029 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8934 (ttp) REVERT: C 190 ARG cc_start: 0.7210 (mtt-85) cc_final: 0.6630 (mtt-85) REVERT: C 281 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7695 (pp20) REVERT: C 509 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6320 (mtt-85) REVERT: C 574 ASP cc_start: 0.7844 (t0) cc_final: 0.7615 (t0) REVERT: C 904 TYR cc_start: 0.8119 (t80) cc_final: 0.7752 (t80) REVERT: C 1101 HIS cc_start: 0.7876 (m90) cc_final: 0.7207 (m90) REVERT: C 1142 GLN cc_start: 0.7177 (mt0) cc_final: 0.6892 (mt0) outliers start: 80 outliers final: 38 residues processed: 289 average time/residue: 0.4957 time to fit residues: 173.6248 Evaluate side-chains 256 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU 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 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 224 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 296 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 281 optimal weight: 0.5980 chunk 152 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 505 HIS A 690 GLN A1125 ASN B 804 GLN B1002 GLN B1119 ASN C 61 ASN C 955 ASN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.182415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132238 restraints weight = 31268.190| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.59 r_work: 0.3441 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26254 Z= 0.127 Angle : 0.597 17.011 35822 Z= 0.304 Chirality : 0.046 0.486 4168 Planarity : 0.004 0.055 4514 Dihedral : 5.477 59.422 4563 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 11.71 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3115 helix: 2.30 (0.19), residues: 723 sheet: 0.26 (0.19), residues: 648 loop : -0.51 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.023 0.001 TYR A 170 PHE 0.021 0.001 PHE A 375 TRP 0.012 0.001 TRP A 452 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00278 (26157) covalent geometry : angle 0.57177 (35575) SS BOND : bond 0.00332 ( 38) SS BOND : angle 1.65662 ( 76) hydrogen bonds : bond 0.04271 ( 985) hydrogen bonds : angle 5.64210 ( 2853) Misc. bond : bond 0.00128 ( 2) link_BETA1-4 : bond 0.00603 ( 21) link_BETA1-4 : angle 1.85311 ( 63) link_NAG-ASN : bond 0.00586 ( 36) link_NAG-ASN : angle 2.54404 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7477 (t80) cc_final: 0.7035 (t80) REVERT: A 129 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7060 (mtpt) REVERT: A 351 TYR cc_start: 0.8330 (p90) cc_final: 0.8070 (p90) REVERT: A 506 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 981 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8602 (mm) REVERT: A 1002 GLN cc_start: 0.8666 (tp40) cc_final: 0.8161 (tt0) REVERT: A 1010 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: B 119 ILE cc_start: 0.6472 (mt) cc_final: 0.6222 (mp) REVERT: B 206 LYS cc_start: 0.7437 (tptt) cc_final: 0.7212 (tptp) REVERT: B 589 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8634 (Cg_endo) REVERT: B 627 ASP cc_start: 0.7898 (m-30) cc_final: 0.7533 (t0) REVERT: C 190 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6571 (mtt-85) REVERT: C 309 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: C 464 PHE cc_start: 0.7055 (m-80) cc_final: 0.6701 (m-80) REVERT: C 509 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6194 (mtt-85) REVERT: C 574 ASP cc_start: 0.7662 (t0) cc_final: 0.7312 (t0) REVERT: C 904 TYR cc_start: 0.8025 (t80) cc_final: 0.7725 (t80) REVERT: C 1101 HIS cc_start: 0.7840 (m90) cc_final: 0.7192 (m90) outliers start: 66 outliers final: 24 residues processed: 276 average time/residue: 0.5275 time to fit residues: 176.1196 Evaluate side-chains 248 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 225 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS B 613 GLN B1002 GLN B1005 GLN C 61 ASN C 360 ASN C 949 GLN C1002 GLN C1142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128167 restraints weight = 31147.862| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.88 r_work: 0.3384 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26254 Z= 0.210 Angle : 0.653 23.077 35822 Z= 0.330 Chirality : 0.048 0.512 4168 Planarity : 0.004 0.056 4514 Dihedral : 5.410 59.415 4563 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 3.18 % Allowed : 11.68 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3115 helix: 2.14 (0.19), residues: 719 sheet: 0.26 (0.19), residues: 653 loop : -0.63 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.022 0.001 TYR C1067 PHE 0.025 0.002 PHE A 392 TRP 0.010 0.002 TRP B 886 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00502 (26157) covalent geometry : angle 0.62859 (35575) SS BOND : bond 0.00521 ( 38) SS BOND : angle 2.06173 ( 76) hydrogen bonds : bond 0.04782 ( 985) hydrogen bonds : angle 5.71942 ( 2853) Misc. bond : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00570 ( 21) link_BETA1-4 : angle 1.72220 ( 63) link_NAG-ASN : bond 0.00482 ( 36) link_NAG-ASN : angle 2.54464 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 225 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8358 (p90) cc_final: 0.8130 (p90) REVERT: A 506 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7870 (mm110) REVERT: A 981 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 1010 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: A 1081 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8838 (mp) REVERT: B 119 ILE cc_start: 0.6563 (mt) cc_final: 0.6327 (mp) REVERT: B 627 ASP cc_start: 0.7846 (m-30) cc_final: 0.7541 (t0) REVERT: B 935 GLN cc_start: 0.8252 (tp40) cc_final: 0.8024 (tt0) REVERT: B 1119 ASN cc_start: 0.8510 (m-40) cc_final: 0.8277 (m110) REVERT: C 32 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: C 177 MET cc_start: 0.2621 (OUTLIER) cc_final: 0.1428 (pmt) REVERT: C 309 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 464 PHE cc_start: 0.7180 (m-80) cc_final: 0.6940 (m-80) REVERT: C 512 VAL cc_start: 0.8738 (t) cc_final: 0.8469 (p) REVERT: C 523 THR cc_start: 0.7101 (p) cc_final: 0.6899 (t) REVERT: C 574 ASP cc_start: 0.7745 (t0) cc_final: 0.7486 (t0) REVERT: C 702 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: C 868 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: C 904 TYR cc_start: 0.8123 (t80) cc_final: 0.7835 (t80) REVERT: C 991 VAL cc_start: 0.8077 (t) cc_final: 0.7809 (p) REVERT: C 1101 HIS cc_start: 0.7909 (m90) cc_final: 0.7290 (m90) outliers start: 88 outliers final: 41 residues processed: 281 average time/residue: 0.5278 time to fit residues: 179.2771 Evaluate side-chains 256 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 425 LEU 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 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 286 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128931 restraints weight = 31344.906| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.83 r_work: 0.3347 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26254 Z= 0.159 Angle : 0.626 19.395 35822 Z= 0.317 Chirality : 0.048 0.824 4168 Planarity : 0.004 0.049 4514 Dihedral : 5.225 56.328 4563 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.75 % Allowed : 13.12 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3115 helix: 2.19 (0.19), residues: 720 sheet: 0.18 (0.19), residues: 660 loop : -0.63 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.024 0.001 TYR A 170 PHE 0.028 0.002 PHE A 515 TRP 0.021 0.001 TRP A 436 HIS 0.028 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00374 (26157) covalent geometry : angle 0.59784 (35575) SS BOND : bond 0.00376 ( 38) SS BOND : angle 1.95001 ( 76) hydrogen bonds : bond 0.04408 ( 985) hydrogen bonds : angle 5.62578 ( 2853) Misc. bond : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00559 ( 21) link_BETA1-4 : angle 1.62009 ( 63) link_NAG-ASN : bond 0.00448 ( 36) link_NAG-ASN : angle 2.80081 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7515 (t80) cc_final: 0.7117 (t80) REVERT: A 226 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 341 VAL cc_start: 0.8923 (m) cc_final: 0.8660 (p) REVERT: A 351 TYR cc_start: 0.8379 (p90) cc_final: 0.8148 (p90) REVERT: A 981 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8746 (mt) REVERT: A 1010 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.6969 (mp10) REVERT: A 1081 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 119 ILE cc_start: 0.6553 (mt) cc_final: 0.6306 (mp) REVERT: B 627 ASP cc_start: 0.7755 (m-30) cc_final: 0.7425 (t0) REVERT: B 844 ILE cc_start: 0.5241 (OUTLIER) cc_final: 0.4702 (mm) REVERT: B 935 GLN cc_start: 0.8251 (tp40) cc_final: 0.8004 (tt0) REVERT: B 1119 ASN cc_start: 0.8504 (m-40) cc_final: 0.8252 (m110) REVERT: C 32 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: C 177 MET cc_start: 0.2602 (OUTLIER) cc_final: 0.1469 (pmt) REVERT: C 309 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: C 464 PHE cc_start: 0.7155 (m-80) cc_final: 0.6897 (m-80) REVERT: C 574 ASP cc_start: 0.7769 (t0) cc_final: 0.7444 (t0) REVERT: C 702 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: C 868 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: C 904 TYR cc_start: 0.8118 (t80) cc_final: 0.7804 (t80) REVERT: C 991 VAL cc_start: 0.8010 (t) cc_final: 0.7749 (p) REVERT: C 1101 HIS cc_start: 0.7939 (m90) cc_final: 0.7281 (m90) outliers start: 76 outliers final: 38 residues processed: 274 average time/residue: 0.4774 time to fit residues: 158.8439 Evaluate side-chains 262 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 130 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129648 restraints weight = 31256.031| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.86 r_work: 0.3361 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26254 Z= 0.149 Angle : 0.603 18.092 35822 Z= 0.305 Chirality : 0.047 0.462 4168 Planarity : 0.004 0.051 4514 Dihedral : 5.050 54.728 4563 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.82 % Allowed : 13.12 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3115 helix: 2.25 (0.19), residues: 725 sheet: 0.07 (0.19), residues: 660 loop : -0.64 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.020 0.001 TYR C1067 PHE 0.033 0.001 PHE B 168 TRP 0.015 0.001 TRP A 436 HIS 0.009 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00347 (26157) covalent geometry : angle 0.57869 (35575) SS BOND : bond 0.00412 ( 38) SS BOND : angle 1.95413 ( 76) hydrogen bonds : bond 0.04243 ( 985) hydrogen bonds : angle 5.53686 ( 2853) Misc. bond : bond 0.00105 ( 2) link_BETA1-4 : bond 0.00552 ( 21) link_BETA1-4 : angle 1.52817 ( 63) link_NAG-ASN : bond 0.00440 ( 36) link_NAG-ASN : angle 2.48330 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7271 (t80) cc_final: 0.6956 (t80) REVERT: A 118 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7552 (tt) REVERT: A 226 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7757 (tt) REVERT: A 341 VAL cc_start: 0.8923 (m) cc_final: 0.8650 (p) REVERT: A 351 TYR cc_start: 0.8349 (p90) cc_final: 0.8133 (p90) REVERT: A 981 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8703 (mt) REVERT: A 1010 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: A 1081 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8799 (mp) REVERT: B 119 ILE cc_start: 0.6466 (mt) cc_final: 0.6223 (mp) REVERT: B 627 ASP cc_start: 0.7784 (m-30) cc_final: 0.7421 (t0) REVERT: B 844 ILE cc_start: 0.5269 (OUTLIER) cc_final: 0.4690 (mm) REVERT: B 935 GLN cc_start: 0.8255 (tp40) cc_final: 0.8002 (tt0) REVERT: B 1092 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 1119 ASN cc_start: 0.8492 (m-40) cc_final: 0.8244 (m110) REVERT: C 32 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: C 188 ASN cc_start: 0.7651 (p0) cc_final: 0.7439 (p0) REVERT: C 309 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: C 464 PHE cc_start: 0.7139 (m-80) cc_final: 0.6871 (m-80) REVERT: C 574 ASP cc_start: 0.7701 (t0) cc_final: 0.7342 (t0) REVERT: C 702 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: C 868 GLU cc_start: 0.8004 (pt0) cc_final: 0.7788 (pp20) REVERT: C 904 TYR cc_start: 0.8081 (t80) cc_final: 0.7764 (t80) REVERT: C 1101 HIS cc_start: 0.7936 (m90) cc_final: 0.7214 (m90) outliers start: 78 outliers final: 41 residues processed: 274 average time/residue: 0.4733 time to fit residues: 158.9785 Evaluate side-chains 265 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 425 LEU 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 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 166 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130151 restraints weight = 31271.379| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.59 r_work: 0.3417 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26254 Z= 0.132 Angle : 0.585 16.845 35822 Z= 0.297 Chirality : 0.046 0.456 4168 Planarity : 0.004 0.050 4514 Dihedral : 4.872 53.432 4563 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.53 % Allowed : 13.92 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3115 helix: 2.33 (0.19), residues: 720 sheet: 0.11 (0.19), residues: 662 loop : -0.63 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.026 0.001 TYR A 170 PHE 0.030 0.001 PHE B 168 TRP 0.014 0.001 TRP A 886 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00303 (26157) covalent geometry : angle 0.56176 (35575) SS BOND : bond 0.00374 ( 38) SS BOND : angle 1.82691 ( 76) hydrogen bonds : bond 0.04049 ( 985) hydrogen bonds : angle 5.45712 ( 2853) Misc. bond : bond 0.00107 ( 2) link_BETA1-4 : bond 0.00574 ( 21) link_BETA1-4 : angle 1.45741 ( 63) link_NAG-ASN : bond 0.00444 ( 36) link_NAG-ASN : angle 2.42848 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 VAL cc_start: 0.8954 (m) cc_final: 0.8704 (p) REVERT: A 351 TYR cc_start: 0.8344 (p90) cc_final: 0.8127 (p90) REVERT: A 981 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8751 (mt) REVERT: A 1010 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: A 1081 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 1092 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: B 119 ILE cc_start: 0.6567 (mt) cc_final: 0.6312 (mp) REVERT: B 271 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: B 627 ASP cc_start: 0.7725 (m-30) cc_final: 0.7415 (t0) REVERT: B 1119 ASN cc_start: 0.8454 (m-40) cc_final: 0.8223 (m110) REVERT: C 32 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: C 188 ASN cc_start: 0.7622 (p0) cc_final: 0.6641 (p0) REVERT: C 190 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6626 (mtt-85) REVERT: C 309 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: C 464 PHE cc_start: 0.7174 (m-80) cc_final: 0.6968 (m-80) REVERT: C 574 ASP cc_start: 0.7689 (t0) cc_final: 0.7378 (t0) REVERT: C 702 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: C 868 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: C 904 TYR cc_start: 0.7993 (t80) cc_final: 0.7684 (t80) REVERT: C 1101 HIS cc_start: 0.7920 (m90) cc_final: 0.7251 (m90) outliers start: 70 outliers final: 44 residues processed: 264 average time/residue: 0.4950 time to fit residues: 160.1596 Evaluate side-chains 264 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 425 LEU 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 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 182 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 119 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 282 optimal weight: 0.0770 chunk 125 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 339 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126200 restraints weight = 31288.559| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.86 r_work: 0.3364 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26254 Z= 0.221 Angle : 0.646 21.307 35822 Z= 0.328 Chirality : 0.049 0.481 4168 Planarity : 0.004 0.046 4514 Dihedral : 5.097 54.759 4563 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.64 % Allowed : 14.24 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3115 helix: 2.12 (0.19), residues: 728 sheet: -0.00 (0.18), residues: 675 loop : -0.68 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.022 0.001 TYR C1067 PHE 0.024 0.002 PHE A 338 TRP 0.015 0.002 TRP A 886 HIS 0.020 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00538 (26157) covalent geometry : angle 0.62367 (35575) SS BOND : bond 0.00528 ( 38) SS BOND : angle 1.98561 ( 76) hydrogen bonds : bond 0.04643 ( 985) hydrogen bonds : angle 5.60457 ( 2853) Misc. bond : bond 0.00109 ( 2) link_BETA1-4 : bond 0.00518 ( 21) link_BETA1-4 : angle 1.49909 ( 63) link_NAG-ASN : bond 0.00449 ( 36) link_NAG-ASN : angle 2.51808 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 218 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8411 (p90) cc_final: 0.8206 (p90) REVERT: A 981 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8842 (mt) REVERT: A 1010 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: A 1081 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 1092 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 119 ILE cc_start: 0.6585 (mt) cc_final: 0.6354 (mp) REVERT: B 153 MET cc_start: 0.2612 (mmp) cc_final: 0.1642 (ptp) REVERT: B 271 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: B 627 ASP cc_start: 0.7788 (m-30) cc_final: 0.7470 (t0) REVERT: B 844 ILE cc_start: 0.5407 (OUTLIER) cc_final: 0.4931 (mm) REVERT: B 935 GLN cc_start: 0.8245 (tp40) cc_final: 0.7993 (tt0) REVERT: B 1119 ASN cc_start: 0.8603 (m-40) cc_final: 0.8383 (m110) REVERT: C 32 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: C 101 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6221 (mp) REVERT: C 188 ASN cc_start: 0.7648 (p0) cc_final: 0.7406 (p0) REVERT: C 574 ASP cc_start: 0.7836 (t0) cc_final: 0.7551 (t0) REVERT: C 702 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: C 904 TYR cc_start: 0.8069 (t80) cc_final: 0.7818 (t80) REVERT: C 1101 HIS cc_start: 0.7968 (m90) cc_final: 0.7350 (m90) outliers start: 73 outliers final: 46 residues processed: 263 average time/residue: 0.5036 time to fit residues: 161.6400 Evaluate side-chains 268 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 425 LEU 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 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 275 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 226 optimal weight: 0.0970 chunk 304 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 360 ASN C 580 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.183020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131480 restraints weight = 31079.701| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.55 r_work: 0.3346 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26254 Z= 0.130 Angle : 0.596 18.335 35822 Z= 0.302 Chirality : 0.046 0.426 4168 Planarity : 0.004 0.048 4514 Dihedral : 4.931 53.443 4563 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 2.21 % Allowed : 14.86 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.15), residues: 3115 helix: 2.27 (0.19), residues: 720 sheet: -0.03 (0.19), residues: 663 loop : -0.65 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.026 0.001 TYR A 170 PHE 0.021 0.001 PHE C 400 TRP 0.016 0.001 TRP A 886 HIS 0.009 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00295 (26157) covalent geometry : angle 0.57205 (35575) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.88407 ( 76) hydrogen bonds : bond 0.04126 ( 985) hydrogen bonds : angle 5.50401 ( 2853) Misc. bond : bond 0.00113 ( 2) link_BETA1-4 : bond 0.00523 ( 21) link_BETA1-4 : angle 1.44866 ( 63) link_NAG-ASN : bond 0.00440 ( 36) link_NAG-ASN : angle 2.48459 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8380 (p90) cc_final: 0.8160 (p90) REVERT: A 981 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8746 (mt) REVERT: A 1010 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: A 1081 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 1092 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 119 ILE cc_start: 0.6496 (mt) cc_final: 0.6241 (mp) REVERT: B 153 MET cc_start: 0.2491 (mmp) cc_final: 0.1566 (ptp) REVERT: B 169 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6880 (tp30) REVERT: B 271 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: B 627 ASP cc_start: 0.7832 (m-30) cc_final: 0.7453 (t0) REVERT: B 676 THR cc_start: 0.7940 (m) cc_final: 0.7736 (p) REVERT: B 935 GLN cc_start: 0.8252 (tp40) cc_final: 0.7969 (tt0) REVERT: B 1119 ASN cc_start: 0.8567 (m-40) cc_final: 0.8339 (m110) REVERT: C 32 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: C 101 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6168 (mp) REVERT: C 188 ASN cc_start: 0.7606 (p0) cc_final: 0.6598 (p0) REVERT: C 190 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6537 (mtt-85) REVERT: C 464 PHE cc_start: 0.7066 (m-80) cc_final: 0.6831 (m-80) REVERT: C 556 ASN cc_start: 0.8710 (m-40) cc_final: 0.7853 (p0) REVERT: C 574 ASP cc_start: 0.7710 (t0) cc_final: 0.7384 (t0) REVERT: C 702 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: C 904 TYR cc_start: 0.8088 (t80) cc_final: 0.7731 (t80) REVERT: C 1101 HIS cc_start: 0.7949 (m90) cc_final: 0.7235 (m90) outliers start: 61 outliers final: 43 residues processed: 253 average time/residue: 0.5143 time to fit residues: 158.7027 Evaluate side-chains 263 residues out of total 2767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 160 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.179823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129211 restraints weight = 31165.967| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.54 r_work: 0.3371 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26254 Z= 0.136 Angle : 0.595 17.381 35822 Z= 0.302 Chirality : 0.046 0.425 4168 Planarity : 0.004 0.047 4514 Dihedral : 4.880 53.088 4563 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 2.28 % Allowed : 14.71 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3115 helix: 2.27 (0.19), residues: 722 sheet: -0.01 (0.19), residues: 669 loop : -0.67 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.020 0.001 TYR B 170 PHE 0.023 0.001 PHE B 168 TRP 0.017 0.001 TRP A 886 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00315 (26157) covalent geometry : angle 0.57304 (35575) SS BOND : bond 0.00377 ( 38) SS BOND : angle 1.80517 ( 76) hydrogen bonds : bond 0.04093 ( 985) hydrogen bonds : angle 5.47279 ( 2853) Misc. bond : bond 0.00107 ( 2) link_BETA1-4 : bond 0.00521 ( 21) link_BETA1-4 : angle 1.43311 ( 63) link_NAG-ASN : bond 0.00415 ( 36) link_NAG-ASN : angle 2.37718 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10799.28 seconds wall clock time: 184 minutes 33.52 seconds (11073.52 seconds total)