Starting phenix.real_space_refine on Sat Jul 4 21:29:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.map" model { file = "/net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyd_64609/07_2026/9uyd_64609.cif" } resolution = 2.7 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= 0.015 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 108 5.16 5 C 14499 2.51 5 N 3708 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22743 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7371 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 52, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "B" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7371 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 52, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "F" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7371 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 52, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.32, per 1000 atoms: 0.23 Number of scatterers: 22743 At special positions: 0 Unit cell: (139.695, 132.66, 172.86, 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 108 16.00 O 4428 8.00 N 3708 7.00 C 14499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS F 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS F 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.02 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG C 1 " - " ASN B 717 " " NAG D 1 " - " ASN B 801 " " NAG E 1 " - " ASN B1074 " " NAG F1301 " - " ASN F 282 " " NAG F1302 " - " ASN F 331 " " NAG F1303 " - " ASN F 343 " " NAG F1304 " - " ASN F 603 " " NAG F1305 " - " ASN F 616 " " NAG F1306 " - " ASN F 657 " " NAG F1307 " - " ASN F 709 " " NAG F1308 " - " ASN F1098 " " NAG F1309 " - " ASN F1134 " " NAG G 1 " - " ASN F 717 " " NAG H 1 " - " ASN F 801 " " NAG I 1 " - " ASN F1074 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5526 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 26.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.847A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.327A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 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 removed outlier: 3.694A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.332A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.508A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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: 4.873A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.490A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.838A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.299A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 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: 3.703A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.608A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.317A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.514A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) 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: 4.889A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.489A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.841A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.633A pdb=" N TRP F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 371 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.338A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.682A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.512A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 941 removed outlier: 4.312A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 removed outlier: 4.526A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL F 952 " --> pdb=" O LEU F 948 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.753A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1146 removed outlier: 4.491A pdb=" N GLU F1144 " --> pdb=" O PRO F1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.554A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.542A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.578A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 197 removed outlier: 6.629A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.925A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.572A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.782A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 removed outlier: 4.589A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.130A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.780A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.756A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.756A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.645A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.568A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.523A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.580A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 188 through 197 removed outlier: 6.603A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.914A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.573A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.781A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 451 through 453 removed outlier: 4.597A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.738A pdb=" N ALA B 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS F 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN B 703 " --> pdb=" O LYS F 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.786A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'F' and resid 28 through 31 Processing sheet with id=AD8, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.561A pdb=" N ASP F 53 " --> pdb=" O ARG F 273 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 93 through 94 removed outlier: 3.523A pdb=" N ALA F 93 " --> pdb=" O TYR F 266 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR F 266 " --> pdb=" O ALA F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 169 through 172 removed outlier: 3.575A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 119 " --> pdb=" O TRP F 104 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN F 121 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 188 through 197 removed outlier: 6.603A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.432A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 325 through 328 removed outlier: 5.577A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY F 566 " --> pdb=" O ASP F 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.782A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 451 through 453 removed outlier: 4.588A pdb=" N TYR F 451 " --> pdb=" O TYR F 495 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.768A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.768A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.595A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 1120 through 1122 953 hydrogen bonds defined for protein. 2616 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: 4.85 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7245 1.35 - 1.47: 5723 1.47 - 1.59: 10126 1.59 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 23226 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG F1303 " pdb=" O5 NAG F1303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 23221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 31118 1.92 - 3.84: 537 3.84 - 5.76: 29 5.76 - 7.68: 6 7.68 - 9.60: 5 Bond angle restraints: 31695 Sorted by residual: angle pdb=" N LEU F 226 " pdb=" CA LEU F 226 " pdb=" C LEU F 226 " ideal model delta sigma weight residual 114.31 108.68 5.63 1.29e+00 6.01e-01 1.91e+01 angle pdb=" N LEU B 226 " pdb=" CA LEU B 226 " pdb=" C LEU B 226 " ideal model delta sigma weight residual 114.31 108.74 5.57 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N LEU A 226 " pdb=" CA LEU A 226 " pdb=" C LEU A 226 " ideal model delta sigma weight residual 114.31 108.75 5.56 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.28 -3.58 1.22e+00 6.72e-01 8.59e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.25 -3.55 1.22e+00 6.72e-01 8.46e+00 ... (remaining 31690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 13198 18.01 - 36.02: 973 36.02 - 54.04: 179 54.04 - 72.05: 32 72.05 - 90.06: 12 Dihedral angle restraints: 14394 sinusoidal: 5859 harmonic: 8535 Sorted by residual: dihedral pdb=" CB CYS B 383 " pdb=" SG CYS B 383 " pdb=" SG CYS F 985 " pdb=" CB CYS F 985 " ideal model delta sinusoidal sigma weight residual -86.00 -149.78 63.78 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CA CYS A 985 " pdb=" C CYS A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA CYS B 985 " pdb=" C CYS B 985 " pdb=" N PRO B 986 " pdb=" CA PRO B 986 " ideal model delta harmonic sigma weight residual 180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 14391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2263 0.029 - 0.058: 880 0.058 - 0.087: 358 0.087 - 0.116: 282 0.116 - 0.145: 60 Chirality restraints: 3843 Sorted by residual: chirality pdb=" CA CYS F 749 " pdb=" N CYS F 749 " pdb=" C CYS F 749 " pdb=" CB CYS F 749 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA CYS B 749 " pdb=" N CYS B 749 " pdb=" C CYS B 749 " pdb=" CB CYS B 749 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 3840 not shown) Planarity restraints: 4074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 43 " 0.019 2.00e-02 2.50e+03 1.47e-02 3.78e+00 pdb=" CG PHE A 43 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 43 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 43 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 43 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 43 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 43 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 43 " -0.018 2.00e-02 2.50e+03 1.42e-02 3.54e+00 pdb=" CG PHE B 43 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 43 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 43 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 43 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 561 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.026 5.00e-02 4.00e+02 ... (remaining 4071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2681 2.75 - 3.29: 20735 3.29 - 3.83: 34595 3.83 - 4.36: 39180 4.36 - 4.90: 71170 Nonbonded interactions: 168361 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR F 37 " pdb=" O LEU F 54 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.225 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.226 3.040 ... (remaining 168356 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 4.340 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.003 0.035 23310 Z= 0.164 Angle : 0.570 9.597 31908 Z= 0.293 Chirality : 0.045 0.145 3843 Planarity : 0.004 0.046 4038 Dihedral : 12.904 90.062 8751 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2856 helix: 2.47 (0.21), residues: 675 sheet: 1.01 (0.22), residues: 561 loop : -1.05 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 577 TYR 0.013 0.001 TYR F1067 PHE 0.032 0.001 PHE A 43 TRP 0.020 0.002 TRP A 886 HIS 0.002 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (23226) covalent geometry : angle 0.56196 / 0.29 (31695) SS BOND : bond 0.00344 / 0.20 ( 39) SS BOND : angle 1.04199 / 0.71 ( 78) hydrogen bonds : bond 0.13790 / 8.77 ( 929) hydrogen bonds : angle 6.02075 / 4.08 ( 2616) link_BETA1-4 : bond 0.00405 / 0.25 ( 9) link_BETA1-4 : angle 1.04544 / 0.64 ( 27) link_NAG-ASN : bond 0.00148 / 0.09 ( 36) link_NAG-ASN : angle 1.51024 / 1.01 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6553 (mpt90) cc_final: 0.6231 (mmt-90) REVERT: A 52 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7939 (tm-30) REVERT: A 207 HIS cc_start: 0.7337 (t-90) cc_final: 0.6556 (m-70) REVERT: A 273 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6692 (mtm180) REVERT: A 309 GLU cc_start: 0.8641 (mp0) cc_final: 0.8320 (mp0) REVERT: A 314 GLN cc_start: 0.8890 (tt0) cc_final: 0.8527 (tt0) REVERT: A 370 ASN cc_start: 0.9207 (m-40) cc_final: 0.8974 (p0) REVERT: A 565 PHE cc_start: 0.8905 (p90) cc_final: 0.8549 (p90) REVERT: A 646 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8103 (mmm-85) REVERT: A 755 GLN cc_start: 0.8867 (mt0) cc_final: 0.8412 (pt0) REVERT: A 773 GLU cc_start: 0.8371 (tt0) cc_final: 0.8139 (tt0) REVERT: A 794 ILE cc_start: 0.8741 (tp) cc_final: 0.8350 (pp) REVERT: A 988 GLU cc_start: 0.8824 (mp0) cc_final: 0.7971 (mp0) REVERT: B 52 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 207 HIS cc_start: 0.7405 (t-90) cc_final: 0.6644 (m-70) REVERT: B 273 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.6734 (mtm180) REVERT: B 309 GLU cc_start: 0.8600 (mp0) cc_final: 0.8306 (mp0) REVERT: B 314 GLN cc_start: 0.8851 (tt0) cc_final: 0.8642 (tt0) REVERT: B 646 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8179 (mmm-85) REVERT: B 755 GLN cc_start: 0.8900 (mt0) cc_final: 0.8552 (pt0) REVERT: B 794 ILE cc_start: 0.8699 (tp) cc_final: 0.8341 (pp) REVERT: B 988 GLU cc_start: 0.8836 (mp0) cc_final: 0.8135 (mp0) REVERT: F 52 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 207 HIS cc_start: 0.6749 (t-90) cc_final: 0.6347 (m-70) REVERT: F 273 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6720 (mtm180) REVERT: F 309 GLU cc_start: 0.8608 (mp0) cc_final: 0.8348 (mp0) REVERT: F 319 ARG cc_start: 0.8276 (ptp90) cc_final: 0.8071 (ptm-80) REVERT: F 370 ASN cc_start: 0.9213 (m-40) cc_final: 0.8939 (p0) REVERT: F 422 ASN cc_start: 0.8876 (m-40) cc_final: 0.8608 (m-40) REVERT: F 646 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8245 (mmm-85) REVERT: F 988 GLU cc_start: 0.8805 (mp0) cc_final: 0.7955 (mp0) REVERT: F 1050 MET cc_start: 0.9507 (ptm) cc_final: 0.9277 (ptm) outliers start: 0 outliers final: 1 residues processed: 263 average time/residue: 0.6231 time to fit residues: 187.2732 Evaluate side-chains 149 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A 804 GLN A 935 GLN F 613 GLN F 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077479 restraints weight = 42210.398| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.07 r_work: 0.2890 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 23310 Z= 0.215 Angle : 0.629 13.567 31908 Z= 0.328 Chirality : 0.048 0.190 3843 Planarity : 0.005 0.053 4038 Dihedral : 5.575 42.275 4022 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.73 % Allowed : 7.55 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2856 helix: 2.41 (0.21), residues: 657 sheet: 0.72 (0.22), residues: 582 loop : -1.13 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.021 0.002 TYR F1067 PHE 0.034 0.002 PHE A 906 TRP 0.020 0.002 TRP F 886 HIS 0.004 0.001 HIS F1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (23226) covalent geometry : angle 0.61282 / 0.32 (31695) SS BOND : bond 0.00452 / 0.26 ( 39) SS BOND : angle 2.27979 / 1.37 ( 78) hydrogen bonds : bond 0.07768 / 5.05 ( 929) hydrogen bonds : angle 5.42993 / 3.68 ( 2616) link_BETA1-4 : bond 0.00274 / 0.16 ( 9) link_BETA1-4 : angle 0.96660 / 0.59 ( 27) link_NAG-ASN : bond 0.00232 / 0.14 ( 36) link_NAG-ASN : angle 1.64456 / 1.08 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.834 Fit side-chains REVERT: A 52 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 207 HIS cc_start: 0.7287 (t-90) cc_final: 0.6666 (m-70) REVERT: A 273 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6634 (mtm180) REVERT: A 309 GLU cc_start: 0.8716 (mp0) cc_final: 0.8375 (mp0) REVERT: A 314 GLN cc_start: 0.8895 (tt0) cc_final: 0.8635 (tt0) REVERT: A 370 ASN cc_start: 0.9236 (m-40) cc_final: 0.8889 (p0) REVERT: A 613 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.9066 (mm-40) REVERT: A 646 ARG cc_start: 0.9055 (mtp85) cc_final: 0.8475 (mmm-85) REVERT: A 988 GLU cc_start: 0.9007 (mp0) cc_final: 0.8221 (mp0) REVERT: B 52 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 131 CYS cc_start: 0.4900 (m) cc_final: 0.4636 (t) REVERT: B 207 HIS cc_start: 0.7413 (t-90) cc_final: 0.6851 (m-70) REVERT: B 273 ARG cc_start: 0.7226 (ttm-80) cc_final: 0.6626 (mtm180) REVERT: B 309 GLU cc_start: 0.8658 (mp0) cc_final: 0.8363 (mp0) REVERT: B 646 ARG cc_start: 0.9106 (mtp85) cc_final: 0.8586 (mmm-85) REVERT: B 755 GLN cc_start: 0.9094 (mt0) cc_final: 0.8580 (pt0) REVERT: B 794 ILE cc_start: 0.8776 (tp) cc_final: 0.8403 (pp) REVERT: B 988 GLU cc_start: 0.9002 (mp0) cc_final: 0.8348 (mp0) REVERT: F 52 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7949 (tm-30) REVERT: F 207 HIS cc_start: 0.7050 (t-90) cc_final: 0.6672 (m-70) REVERT: F 273 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6618 (mtm180) REVERT: F 319 ARG cc_start: 0.8404 (ptp90) cc_final: 0.8130 (ptm-80) REVERT: F 370 ASN cc_start: 0.9254 (m-40) cc_final: 0.8887 (p0) REVERT: F 613 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9036 (mm-40) REVERT: F 646 ARG cc_start: 0.9129 (mtp85) cc_final: 0.8635 (mmm-85) REVERT: F 988 GLU cc_start: 0.8980 (mp0) cc_final: 0.8233 (mp0) outliers start: 41 outliers final: 16 residues processed: 179 average time/residue: 0.6210 time to fit residues: 126.9112 Evaluate side-chains 144 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 613 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 114 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 277 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078280 restraints weight = 42102.362| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.93 r_work: 0.2936 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23310 Z= 0.145 Angle : 0.550 14.134 31908 Z= 0.285 Chirality : 0.045 0.165 3843 Planarity : 0.004 0.050 4038 Dihedral : 4.949 34.906 4020 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.98 % Allowed : 9.54 % Favored : 88.48 % 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 are not related in a simple way. whole: 0.40 (0.16), residues: 2856 helix: 2.82 (0.21), residues: 633 sheet: 0.80 (0.22), residues: 552 loop : -1.00 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.017 0.001 TYR F1067 PHE 0.024 0.001 PHE F 43 TRP 0.013 0.001 TRP F 886 HIS 0.003 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (23226) covalent geometry : angle 0.53546 / 0.28 (31695) SS BOND : bond 0.00381 / 0.22 ( 39) SS BOND : angle 1.86662 / 1.13 ( 78) hydrogen bonds : bond 0.06690 / 4.32 ( 929) hydrogen bonds : angle 5.19419 / 3.52 ( 2616) link_BETA1-4 : bond 0.00273 / 0.17 ( 9) link_BETA1-4 : angle 0.96460 / 0.59 ( 27) link_NAG-ASN : bond 0.00169 / 0.10 ( 36) link_NAG-ASN : angle 1.56515 / 1.04 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.890 Fit side-chains REVERT: A 52 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 207 HIS cc_start: 0.7303 (t-90) cc_final: 0.6702 (m-70) REVERT: A 273 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6685 (mtm180) REVERT: A 309 GLU cc_start: 0.8694 (mp0) cc_final: 0.8390 (mp0) REVERT: A 314 GLN cc_start: 0.8939 (tt0) cc_final: 0.8688 (tt0) REVERT: A 370 ASN cc_start: 0.9202 (m-40) cc_final: 0.8848 (p0) REVERT: A 613 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9075 (mm-40) REVERT: A 646 ARG cc_start: 0.9073 (mtp85) cc_final: 0.8495 (mmm-85) REVERT: A 988 GLU cc_start: 0.9043 (mp0) cc_final: 0.8378 (mp0) REVERT: B 52 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 207 HIS cc_start: 0.7399 (t-90) cc_final: 0.6754 (m-70) REVERT: B 273 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6654 (mtm180) REVERT: B 309 GLU cc_start: 0.8629 (mp0) cc_final: 0.8362 (mp0) REVERT: B 646 ARG cc_start: 0.9085 (mtp85) cc_final: 0.8564 (mmm-85) REVERT: B 755 GLN cc_start: 0.9103 (mt0) cc_final: 0.8595 (pt0) REVERT: B 794 ILE cc_start: 0.8792 (tp) cc_final: 0.8416 (pp) REVERT: B 988 GLU cc_start: 0.9030 (mp0) cc_final: 0.8358 (mp0) REVERT: F 52 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 207 HIS cc_start: 0.7091 (t-90) cc_final: 0.6695 (m-70) REVERT: F 273 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6660 (mtm180) REVERT: F 309 GLU cc_start: 0.8752 (mp0) cc_final: 0.8502 (mp0) REVERT: F 319 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8161 (ptm-80) REVERT: F 370 ASN cc_start: 0.9199 (m-40) cc_final: 0.8825 (p0) REVERT: F 646 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8607 (mmm-85) REVERT: F 988 GLU cc_start: 0.9008 (mp0) cc_final: 0.8291 (mp0) REVERT: F 1050 MET cc_start: 0.9529 (ptm) cc_final: 0.9222 (ptm) outliers start: 47 outliers final: 24 residues processed: 174 average time/residue: 0.5840 time to fit residues: 117.8872 Evaluate side-chains 151 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 933 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 279 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 278 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078695 restraints weight = 42449.764| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.96 r_work: 0.2936 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23310 Z= 0.135 Angle : 0.537 12.754 31908 Z= 0.277 Chirality : 0.045 0.156 3843 Planarity : 0.004 0.049 4038 Dihedral : 4.480 33.962 4020 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.15 % Allowed : 10.25 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2856 helix: 2.69 (0.21), residues: 654 sheet: 0.79 (0.22), residues: 576 loop : -0.96 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.017 0.001 TYR F1067 PHE 0.019 0.001 PHE F 43 TRP 0.010 0.001 TRP F 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (23226) covalent geometry : angle 0.52409 / 0.27 (31695) SS BOND : bond 0.00465 / 0.26 ( 39) SS BOND : angle 1.65897 / 1.01 ( 78) hydrogen bonds : bond 0.06293 / 4.07 ( 929) hydrogen bonds : angle 5.03715 / 3.41 ( 2616) link_BETA1-4 : bond 0.00275 / 0.16 ( 9) link_BETA1-4 : angle 0.91744 / 0.55 ( 27) link_NAG-ASN : bond 0.00157 / 0.09 ( 36) link_NAG-ASN : angle 1.53861 / 1.03 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.831 Fit side-chains REVERT: A 52 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 207 HIS cc_start: 0.7246 (t-90) cc_final: 0.6730 (m-70) REVERT: A 273 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6679 (mtm180) REVERT: A 309 GLU cc_start: 0.8656 (mp0) cc_final: 0.8354 (mp0) REVERT: A 314 GLN cc_start: 0.8916 (tt0) cc_final: 0.8684 (tt0) REVERT: A 370 ASN cc_start: 0.9187 (m-40) cc_final: 0.8825 (p0) REVERT: A 646 ARG cc_start: 0.9074 (mtp85) cc_final: 0.8487 (mmm-85) REVERT: A 988 GLU cc_start: 0.9004 (mp0) cc_final: 0.8368 (mp0) REVERT: B 52 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 207 HIS cc_start: 0.7225 (t-90) cc_final: 0.6811 (m-70) REVERT: B 273 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6669 (mtm180) REVERT: B 309 GLU cc_start: 0.8611 (mp0) cc_final: 0.8364 (mp0) REVERT: B 646 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8519 (mmm-85) REVERT: B 755 GLN cc_start: 0.9094 (mt0) cc_final: 0.8587 (pt0) REVERT: B 933 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8582 (mtpt) REVERT: B 988 GLU cc_start: 0.9023 (mp0) cc_final: 0.8365 (mp0) REVERT: F 41 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6915 (tptt) REVERT: F 52 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7974 (tm-30) REVERT: F 207 HIS cc_start: 0.7071 (t-90) cc_final: 0.6687 (m-70) REVERT: F 273 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6567 (mtm180) REVERT: F 309 GLU cc_start: 0.8744 (mp0) cc_final: 0.8487 (mp0) REVERT: F 319 ARG cc_start: 0.8400 (ptp90) cc_final: 0.8067 (ptm-80) REVERT: F 370 ASN cc_start: 0.9197 (m-40) cc_final: 0.8821 (p0) REVERT: F 646 ARG cc_start: 0.9077 (mtp85) cc_final: 0.8586 (mmm-85) REVERT: F 988 GLU cc_start: 0.9002 (mp0) cc_final: 0.8289 (mp0) REVERT: F 1050 MET cc_start: 0.9504 (ptm) cc_final: 0.9221 (ptm) outliers start: 51 outliers final: 29 residues processed: 176 average time/residue: 0.5803 time to fit residues: 117.7700 Evaluate side-chains 155 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 933 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 143 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 287 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 272 optimal weight: 0.0000 chunk 64 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN F 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079435 restraints weight = 42309.268| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.94 r_work: 0.2964 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23310 Z= 0.117 Angle : 0.517 12.068 31908 Z= 0.266 Chirality : 0.044 0.157 3843 Planarity : 0.004 0.048 4038 Dihedral : 4.259 33.453 4020 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.19 % Allowed : 10.72 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2856 helix: 2.82 (0.21), residues: 654 sheet: 0.75 (0.21), residues: 594 loop : -0.93 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.016 0.001 TYR F1067 PHE 0.017 0.001 PHE F 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (23226) covalent geometry : angle 0.50506 / 0.26 (31695) SS BOND : bond 0.00447 / 0.28 ( 39) SS BOND : angle 1.49382 / 0.91 ( 78) hydrogen bonds : bond 0.05797 / 3.74 ( 929) hydrogen bonds : angle 4.88401 / 3.30 ( 2616) link_BETA1-4 : bond 0.00299 / 0.18 ( 9) link_BETA1-4 : angle 0.88922 / 0.54 ( 27) link_NAG-ASN : bond 0.00160 / 0.09 ( 36) link_NAG-ASN : angle 1.49164 / 1.00 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.899 Fit side-chains REVERT: A 52 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 207 HIS cc_start: 0.7252 (t-90) cc_final: 0.6731 (m-70) REVERT: A 273 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6677 (mtm180) REVERT: A 309 GLU cc_start: 0.8602 (mp0) cc_final: 0.8327 (mp0) REVERT: A 314 GLN cc_start: 0.8862 (tt0) cc_final: 0.8575 (tt0) REVERT: A 370 ASN cc_start: 0.9221 (m-40) cc_final: 0.8866 (p0) REVERT: A 613 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8956 (mp10) REVERT: A 646 ARG cc_start: 0.9044 (mtp85) cc_final: 0.8462 (mmm-85) REVERT: A 988 GLU cc_start: 0.9005 (mp0) cc_final: 0.8362 (mp0) REVERT: B 52 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 207 HIS cc_start: 0.7224 (t-90) cc_final: 0.6800 (m-70) REVERT: B 273 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6768 (mtm180) REVERT: B 309 GLU cc_start: 0.8569 (mp0) cc_final: 0.8318 (mp0) REVERT: B 646 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8507 (mmm-85) REVERT: B 755 GLN cc_start: 0.9094 (mt0) cc_final: 0.8595 (pt0) REVERT: B 933 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8586 (mtpt) REVERT: B 988 GLU cc_start: 0.9012 (mp0) cc_final: 0.8458 (mp0) REVERT: F 41 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6768 (tptt) REVERT: F 207 HIS cc_start: 0.7091 (t-90) cc_final: 0.6712 (m-70) REVERT: F 273 ARG cc_start: 0.7150 (ttm-80) cc_final: 0.6516 (mtm180) REVERT: F 309 GLU cc_start: 0.8723 (mp0) cc_final: 0.8471 (mp0) REVERT: F 319 ARG cc_start: 0.8352 (ptp90) cc_final: 0.7989 (ptm-80) REVERT: F 370 ASN cc_start: 0.9222 (m-40) cc_final: 0.8872 (p0) REVERT: F 646 ARG cc_start: 0.9053 (mtp85) cc_final: 0.8557 (mmm-85) REVERT: F 988 GLU cc_start: 0.8999 (mp0) cc_final: 0.8267 (mp0) REVERT: F 1050 MET cc_start: 0.9483 (ptm) cc_final: 0.9178 (ptm) outliers start: 52 outliers final: 31 residues processed: 174 average time/residue: 0.5929 time to fit residues: 119.1491 Evaluate side-chains 162 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 933 LYS Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 179 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 235 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A 613 GLN B 564 GLN F 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079979 restraints weight = 42410.754| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.95 r_work: 0.2959 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 23310 Z= 0.112 Angle : 0.513 16.533 31908 Z= 0.263 Chirality : 0.044 0.154 3843 Planarity : 0.004 0.048 4038 Dihedral : 4.136 32.938 4020 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.11 % Allowed : 11.39 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2856 helix: 2.76 (0.21), residues: 663 sheet: 0.81 (0.21), residues: 594 loop : -0.94 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.016 0.001 TYR F1067 PHE 0.015 0.001 PHE F 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (23226) covalent geometry : angle 0.50130 / 0.26 (31695) SS BOND : bond 0.00468 / 0.26 ( 39) SS BOND : angle 1.45380 / 0.87 ( 78) hydrogen bonds : bond 0.05593 / 3.61 ( 929) hydrogen bonds : angle 4.81155 / 3.25 ( 2616) link_BETA1-4 : bond 0.00309 / 0.19 ( 9) link_BETA1-4 : angle 0.89237 / 0.53 ( 27) link_NAG-ASN : bond 0.00166 / 0.10 ( 36) link_NAG-ASN : angle 1.47477 / 0.99 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.822 Fit side-chains REVERT: A 52 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 207 HIS cc_start: 0.7263 (t-90) cc_final: 0.6761 (m-70) REVERT: A 273 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6644 (mtm180) REVERT: A 309 GLU cc_start: 0.8590 (mp0) cc_final: 0.8294 (mp0) REVERT: A 314 GLN cc_start: 0.8858 (tt0) cc_final: 0.8581 (tt0) REVERT: A 370 ASN cc_start: 0.9222 (m-40) cc_final: 0.8864 (p0) REVERT: A 613 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8991 (mp10) REVERT: A 646 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8763 (tpp80) REVERT: A 988 GLU cc_start: 0.8990 (mp0) cc_final: 0.8353 (mp0) REVERT: B 52 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 207 HIS cc_start: 0.7211 (t-90) cc_final: 0.6849 (m-70) REVERT: B 273 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6779 (mtm180) REVERT: B 309 GLU cc_start: 0.8565 (mp0) cc_final: 0.8310 (mp0) REVERT: B 646 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8686 (tpp80) REVERT: B 755 GLN cc_start: 0.9083 (mt0) cc_final: 0.8594 (pt0) REVERT: B 933 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8576 (mtpt) REVERT: B 988 GLU cc_start: 0.8966 (mp0) cc_final: 0.8334 (mp0) REVERT: F 41 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6763 (tptt) REVERT: F 207 HIS cc_start: 0.7098 (t-90) cc_final: 0.6732 (m-70) REVERT: F 273 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6603 (mtm180) REVERT: F 309 GLU cc_start: 0.8707 (mp0) cc_final: 0.8455 (mp0) REVERT: F 319 ARG cc_start: 0.8316 (ptp90) cc_final: 0.7978 (ptm-80) REVERT: F 370 ASN cc_start: 0.9222 (m-40) cc_final: 0.8870 (p0) REVERT: F 582 LEU cc_start: 0.9258 (mm) cc_final: 0.9020 (mm) REVERT: F 646 ARG cc_start: 0.9056 (mtp85) cc_final: 0.8555 (mmm-85) REVERT: F 988 GLU cc_start: 0.8972 (mp0) cc_final: 0.8234 (mp0) REVERT: F 1050 MET cc_start: 0.9476 (ptm) cc_final: 0.9190 (ptm) outliers start: 50 outliers final: 33 residues processed: 172 average time/residue: 0.6003 time to fit residues: 118.5009 Evaluate side-chains 165 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 933 LYS Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 250 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 163 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS B 564 GLN F 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078715 restraints weight = 42338.636| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.95 r_work: 0.2940 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 23310 Z= 0.138 Angle : 0.533 14.615 31908 Z= 0.272 Chirality : 0.044 0.150 3843 Planarity : 0.004 0.046 4038 Dihedral : 4.146 32.781 4020 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.36 % Allowed : 11.56 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2856 helix: 2.75 (0.21), residues: 663 sheet: 0.78 (0.21), residues: 594 loop : -0.96 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.017 0.001 TYR F1067 PHE 0.016 0.001 PHE F 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (23226) covalent geometry : angle 0.52067 / 0.27 (31695) SS BOND : bond 0.00509 / 0.32 ( 39) SS BOND : angle 1.57517 / 0.95 ( 78) hydrogen bonds : bond 0.06138 / 3.97 ( 929) hydrogen bonds : angle 4.87050 / 3.30 ( 2616) link_BETA1-4 : bond 0.00247 / 0.16 ( 9) link_BETA1-4 : angle 0.92750 / 0.56 ( 27) link_NAG-ASN : bond 0.00157 / 0.09 ( 36) link_NAG-ASN : angle 1.50287 / 1.01 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.821 Fit side-chains REVERT: A 52 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 207 HIS cc_start: 0.7153 (t-90) cc_final: 0.6811 (m-70) REVERT: A 273 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.6656 (mtm180) REVERT: A 309 GLU cc_start: 0.8571 (mp0) cc_final: 0.8296 (mp0) REVERT: A 314 GLN cc_start: 0.8870 (tt0) cc_final: 0.8659 (tt0) REVERT: A 370 ASN cc_start: 0.9213 (m-40) cc_final: 0.8838 (p0) REVERT: A 646 ARG cc_start: 0.9060 (mtp85) cc_final: 0.8766 (tpp80) REVERT: A 988 GLU cc_start: 0.9017 (mp0) cc_final: 0.8363 (mp0) REVERT: B 52 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 207 HIS cc_start: 0.7222 (t-90) cc_final: 0.6866 (m-70) REVERT: B 273 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.6742 (mtm180) REVERT: B 309 GLU cc_start: 0.8584 (mp0) cc_final: 0.8318 (mp0) REVERT: B 646 ARG cc_start: 0.9062 (mtp85) cc_final: 0.8510 (mmm-85) REVERT: B 755 GLN cc_start: 0.9099 (mt0) cc_final: 0.8607 (pt0) REVERT: B 988 GLU cc_start: 0.9005 (mp0) cc_final: 0.8420 (mp0) REVERT: F 207 HIS cc_start: 0.7160 (t-90) cc_final: 0.6758 (m-70) REVERT: F 273 ARG cc_start: 0.7220 (ttm-80) cc_final: 0.6537 (mtm180) REVERT: F 309 GLU cc_start: 0.8726 (mp0) cc_final: 0.8468 (mp0) REVERT: F 319 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7990 (ptm-80) REVERT: F 370 ASN cc_start: 0.9229 (m-40) cc_final: 0.8869 (p0) REVERT: F 646 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8556 (mmm-85) REVERT: F 988 GLU cc_start: 0.8985 (mp0) cc_final: 0.8210 (mp0) REVERT: F 1050 MET cc_start: 0.9487 (ptm) cc_final: 0.9181 (ptm) outliers start: 56 outliers final: 40 residues processed: 169 average time/residue: 0.6043 time to fit residues: 118.1346 Evaluate side-chains 163 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 933 LYS Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 764 ASN F 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079531 restraints weight = 42165.701| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.96 r_work: 0.2951 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23310 Z= 0.121 Angle : 0.526 14.024 31908 Z= 0.268 Chirality : 0.044 0.156 3843 Planarity : 0.004 0.047 4038 Dihedral : 4.061 32.778 4020 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.98 % Allowed : 12.03 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2856 helix: 2.76 (0.21), residues: 663 sheet: 0.84 (0.21), residues: 594 loop : -0.94 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.016 0.001 TYR F1067 PHE 0.016 0.001 PHE F 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (23226) covalent geometry : angle 0.51216 / 0.26 (31695) SS BOND : bond 0.00447 / 0.28 ( 39) SS BOND : angle 1.78650 / 1.02 ( 78) hydrogen bonds : bond 0.05788 / 3.73 ( 929) hydrogen bonds : angle 4.79444 / 3.24 ( 2616) link_BETA1-4 : bond 0.00292 / 0.18 ( 9) link_BETA1-4 : angle 0.90082 / 0.54 ( 27) link_NAG-ASN : bond 0.00167 / 0.10 ( 36) link_NAG-ASN : angle 1.46737 / 0.98 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.949 Fit side-chains REVERT: A 52 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 207 HIS cc_start: 0.7169 (t-90) cc_final: 0.6812 (m-70) REVERT: A 273 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.6649 (mtm180) REVERT: A 309 GLU cc_start: 0.8557 (mp0) cc_final: 0.8284 (mp0) REVERT: A 314 GLN cc_start: 0.8859 (tt0) cc_final: 0.8652 (tt0) REVERT: A 370 ASN cc_start: 0.9208 (m-40) cc_final: 0.8832 (p0) REVERT: A 646 ARG cc_start: 0.9074 (mtp85) cc_final: 0.8791 (tpp80) REVERT: A 988 GLU cc_start: 0.9014 (mp0) cc_final: 0.8386 (mp0) REVERT: B 52 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 207 HIS cc_start: 0.7231 (t-90) cc_final: 0.6877 (m-70) REVERT: B 273 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.6734 (mtm180) REVERT: B 309 GLU cc_start: 0.8563 (mp0) cc_final: 0.8301 (mp0) REVERT: B 646 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8606 (tpp80) REVERT: B 729 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9158 (t) REVERT: B 755 GLN cc_start: 0.9094 (mt0) cc_final: 0.8616 (pt0) REVERT: B 988 GLU cc_start: 0.8986 (mp0) cc_final: 0.8404 (mp0) REVERT: F 207 HIS cc_start: 0.7168 (t-90) cc_final: 0.6766 (m-70) REVERT: F 273 ARG cc_start: 0.7150 (ttm-80) cc_final: 0.6460 (mtm180) REVERT: F 309 GLU cc_start: 0.8719 (mp0) cc_final: 0.8460 (mp0) REVERT: F 319 ARG cc_start: 0.8334 (ptp90) cc_final: 0.7999 (ptm-80) REVERT: F 370 ASN cc_start: 0.9227 (m-40) cc_final: 0.8866 (p0) REVERT: F 646 ARG cc_start: 0.9080 (mtp85) cc_final: 0.8586 (mmm-85) REVERT: F 988 GLU cc_start: 0.8991 (mp0) cc_final: 0.8220 (mp0) REVERT: F 1050 MET cc_start: 0.9473 (ptm) cc_final: 0.9178 (ptm) outliers start: 47 outliers final: 33 residues processed: 170 average time/residue: 0.6024 time to fit residues: 118.4333 Evaluate side-chains 162 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 8 optimal weight: 0.9990 chunk 195 optimal weight: 0.0020 chunk 168 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN F 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080067 restraints weight = 42378.185| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.96 r_work: 0.2963 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23310 Z= 0.115 Angle : 0.522 14.010 31908 Z= 0.266 Chirality : 0.044 0.155 3843 Planarity : 0.004 0.048 4038 Dihedral : 3.989 32.417 4020 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.86 % Allowed : 12.62 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2856 helix: 2.79 (0.21), residues: 663 sheet: 0.87 (0.21), residues: 594 loop : -0.91 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.016 0.001 TYR F1067 PHE 0.013 0.001 PHE B 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (23226) covalent geometry : angle 0.50749 / 0.26 (31695) SS BOND : bond 0.00408 / 0.25 ( 39) SS BOND : angle 1.89739 / 1.10 ( 78) hydrogen bonds : bond 0.05566 / 3.60 ( 929) hydrogen bonds : angle 4.73884 / 3.20 ( 2616) link_BETA1-4 : bond 0.00276 / 0.17 ( 9) link_BETA1-4 : angle 0.88842 / 0.53 ( 27) link_NAG-ASN : bond 0.00166 / 0.10 ( 36) link_NAG-ASN : angle 1.44225 / 0.97 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.886 Fit side-chains REVERT: A 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 207 HIS cc_start: 0.7155 (t-90) cc_final: 0.6804 (m-70) REVERT: A 273 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.6656 (mtm180) REVERT: A 309 GLU cc_start: 0.8566 (mp0) cc_final: 0.8289 (mp0) REVERT: A 314 GLN cc_start: 0.8846 (tt0) cc_final: 0.8642 (tt0) REVERT: A 370 ASN cc_start: 0.9208 (m-40) cc_final: 0.8829 (p0) REVERT: A 646 ARG cc_start: 0.9059 (mtp85) cc_final: 0.8773 (tpp80) REVERT: A 988 GLU cc_start: 0.9029 (mp0) cc_final: 0.8423 (mp0) REVERT: B 52 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 207 HIS cc_start: 0.7136 (t-90) cc_final: 0.6880 (m-70) REVERT: B 273 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6617 (mtm180) REVERT: B 309 GLU cc_start: 0.8552 (mp0) cc_final: 0.8303 (mp0) REVERT: B 646 ARG cc_start: 0.9083 (mtp85) cc_final: 0.8614 (tpp80) REVERT: B 755 GLN cc_start: 0.9091 (mt0) cc_final: 0.8686 (pt0) REVERT: B 988 GLU cc_start: 0.8955 (mp0) cc_final: 0.8367 (mp0) REVERT: F 207 HIS cc_start: 0.7160 (t-90) cc_final: 0.6763 (m-70) REVERT: F 273 ARG cc_start: 0.7172 (ttm-80) cc_final: 0.6462 (mtm180) REVERT: F 309 GLU cc_start: 0.8709 (mp0) cc_final: 0.8455 (mp0) REVERT: F 319 ARG cc_start: 0.8330 (ptp90) cc_final: 0.7993 (ptm-80) REVERT: F 370 ASN cc_start: 0.9222 (m-40) cc_final: 0.8864 (p0) REVERT: F 646 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8583 (mmm-85) REVERT: F 729 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9147 (t) REVERT: F 988 GLU cc_start: 0.8970 (mp0) cc_final: 0.8200 (mp0) REVERT: F 1050 MET cc_start: 0.9460 (ptm) cc_final: 0.9178 (ptm) outliers start: 44 outliers final: 31 residues processed: 166 average time/residue: 0.5912 time to fit residues: 113.4114 Evaluate side-chains 158 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 933 LYS Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 112 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 136 optimal weight: 0.0070 chunk 226 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 178 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.127850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080039 restraints weight = 42324.535| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.94 r_work: 0.2974 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23310 Z= 0.115 Angle : 0.523 13.969 31908 Z= 0.267 Chirality : 0.044 0.159 3843 Planarity : 0.004 0.047 4038 Dihedral : 3.957 32.018 4020 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.81 % Allowed : 12.66 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2856 helix: 2.77 (0.22), residues: 663 sheet: 0.89 (0.21), residues: 594 loop : -0.90 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.016 0.001 TYR F1067 PHE 0.013 0.001 PHE B 43 TRP 0.009 0.001 TRP F 436 HIS 0.003 0.000 HIS F1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (23226) covalent geometry : angle 0.50868 / 0.26 (31695) SS BOND : bond 0.00402 / 0.25 ( 39) SS BOND : angle 1.91328 / 1.12 ( 78) hydrogen bonds : bond 0.05509 / 3.55 ( 929) hydrogen bonds : angle 4.70723 / 3.18 ( 2616) link_BETA1-4 : bond 0.00331 / 0.20 ( 9) link_BETA1-4 : angle 0.89968 / 0.54 ( 27) link_NAG-ASN : bond 0.00168 / 0.10 ( 36) link_NAG-ASN : angle 1.43146 / 0.96 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.844 Fit side-chains REVERT: A 207 HIS cc_start: 0.7147 (t-90) cc_final: 0.6874 (m-70) REVERT: A 273 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6701 (mtm180) REVERT: A 309 GLU cc_start: 0.8553 (mp0) cc_final: 0.8279 (mp0) REVERT: A 314 GLN cc_start: 0.8819 (tt0) cc_final: 0.8614 (tt0) REVERT: A 324 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: A 370 ASN cc_start: 0.9207 (m-40) cc_final: 0.8829 (p0) REVERT: A 646 ARG cc_start: 0.9071 (mtp85) cc_final: 0.8784 (tpp80) REVERT: A 988 GLU cc_start: 0.8982 (mp0) cc_final: 0.8369 (mp0) REVERT: A 990 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 52 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 207 HIS cc_start: 0.7117 (t-90) cc_final: 0.6877 (m-70) REVERT: B 273 ARG cc_start: 0.7135 (ttm-80) cc_final: 0.6620 (mtm180) REVERT: B 309 GLU cc_start: 0.8541 (mp0) cc_final: 0.8291 (mp0) REVERT: B 646 ARG cc_start: 0.9077 (mtp85) cc_final: 0.8609 (tpp80) REVERT: B 729 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9158 (t) REVERT: B 755 GLN cc_start: 0.9094 (mt0) cc_final: 0.8695 (pt0) REVERT: B 988 GLU cc_start: 0.8964 (mp0) cc_final: 0.8427 (mp0) REVERT: F 207 HIS cc_start: 0.7180 (t-90) cc_final: 0.6804 (m-70) REVERT: F 273 ARG cc_start: 0.7155 (ttm-80) cc_final: 0.6453 (mtm180) REVERT: F 309 GLU cc_start: 0.8699 (mp0) cc_final: 0.8446 (mp0) REVERT: F 319 ARG cc_start: 0.8305 (ptp90) cc_final: 0.7949 (ptm-80) REVERT: F 370 ASN cc_start: 0.9219 (m-40) cc_final: 0.8862 (p0) REVERT: F 646 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8568 (mmm-85) REVERT: F 729 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9153 (t) REVERT: F 988 GLU cc_start: 0.8972 (mp0) cc_final: 0.8214 (mp0) REVERT: F 1050 MET cc_start: 0.9474 (ptm) cc_final: 0.9232 (ptm) outliers start: 43 outliers final: 31 residues processed: 164 average time/residue: 0.5811 time to fit residues: 110.1863 Evaluate side-chains 161 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 933 LYS Chi-restraints excluded: chain F residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 206 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 287 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 935 GLN F 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078501 restraints weight = 42358.461| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.96 r_work: 0.2930 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23310 Z= 0.146 Angle : 0.550 13.511 31908 Z= 0.283 Chirality : 0.045 0.156 3843 Planarity : 0.004 0.048 4038 Dihedral : 4.054 32.375 4020 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.90 % Allowed : 12.91 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2856 helix: 2.67 (0.22), residues: 663 sheet: 0.81 (0.21), residues: 594 loop : -0.96 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.017 0.001 TYR F1067 PHE 0.015 0.001 PHE B 43 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (23226) covalent geometry : angle 0.53485 / 0.28 (31695) SS BOND : bond 0.00425 / 0.26 ( 39) SS BOND : angle 2.01656 / 1.19 ( 78) hydrogen bonds : bond 0.06366 / 4.13 ( 929) hydrogen bonds : angle 4.85388 / 3.29 ( 2616) link_BETA1-4 : bond 0.00266 / 0.16 ( 9) link_BETA1-4 : angle 0.95078 / 0.57 ( 27) link_NAG-ASN : bond 0.00158 / 0.09 ( 36) link_NAG-ASN : angle 1.50622 / 1.01 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9117.74 seconds wall clock time: 155 minutes 31.41 seconds (9331.41 seconds total)