Starting phenix.real_space_refine on Fri Feb 6 16:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w75_65717/02_2026/9w75_65717.map" } resolution = 2.13 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= 0.001 sd= 0.030 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 117 5.16 5 C 16492 2.51 5 N 4229 2.21 5 O 5159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25997 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8284 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 3 Chain: "B" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8284 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 3 Chain: "C" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8284 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 3 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.62, per 1000 atoms: 0.22 Number of scatterers: 25997 At special positions: 0 Unit cell: (138.57, 130.2, 165.54, 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 117 16.00 O 5159 8.00 N 4229 7.00 C 16492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 722 " distance=2.02 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 813 " distance=2.03 Simple disulfide: pdb=" SG CYS A 994 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1088 " distance=2.04 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 146 " distance=2.04 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 406 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 813 " distance=2.03 Simple disulfide: pdb=" SG CYS B 994 " - pdb=" SG CYS B1005 " distance=2.02 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1088 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 555 " distance=2.03 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 722 " distance=2.03 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS C 711 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 813 " distance=2.03 Simple disulfide: pdb=" SG CYS C 994 " - pdb=" SG CYS C1005 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1088 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN K 4 " - " MAN K 5 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1302 " - " ASN A 581 " " NAG A1303 " - " ASN A 103 " " NAG A1304 " - " ASN A 59 " " NAG A1305 " - " ASN A 256 " " NAG A1306 " - " ASN A 622 " " NAG A1307 " - " ASN A 763 " " NAG A1308 " - " ASN A 679 " " NAG A1309 " - " ASN A 671 " " NAG A1310 " - " ASN A1036 " " NAG A1311 " - " ASN A1060 " " NAG A1312 " - " ASN A 145 " " NAG B1303 " - " ASN B 145 " " NAG B1304 " - " ASN B 103 " " NAG B1305 " - " ASN B 59 " " NAG B1306 " - " ASN B 581 " " NAG B1307 " - " ASN B 256 " " NAG B1308 " - " ASN B 622 " " NAG B1309 " - " ASN B 763 " " NAG B1310 " - " ASN B 679 " " NAG B1311 " - " ASN B 671 " " NAG B1312 " - " ASN B1036 " " NAG B1313 " - " ASN B1060 " " NAG C1303 " - " ASN C 305 " " NAG C1304 " - " ASN C 581 " " NAG C1305 " - " ASN C 149 " " NAG C1306 " - " ASN C 103 " " NAG C1307 " - " ASN C 59 " " NAG C1308 " - " ASN C 256 " " NAG C1309 " - " ASN C 622 " " NAG C1310 " - " ASN C 763 " " NAG C1311 " - " ASN C 679 " " NAG C1312 " - " ASN C 671 " " NAG C1313 " - " ASN C1036 " " NAG C1314 " - " ASN C1060 " " NAG D 1 " - " ASN A 305 " " NAG E 1 " - " ASN A 317 " " NAG F 1 " - " ASN A 344 " " NAG G 1 " - " ASN A 218 " " NAG H 1 " - " ASN A 149 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 344 " " NAG K 1 " - " ASN B 218 " " NAG L 1 " - " ASN B 305 " " NAG M 1 " - " ASN B 149 " " NAG N 1 " - " ASN C 344 " " NAG O 1 " - " ASN C 145 " " NAG P 1 " - " ASN C 218 " " NAG Q 1 " - " ASN C 317 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 24.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 311 through 317 Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.617A pdb=" N TRP A 327 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.733A pdb=" N LEU A 342 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.500A pdb=" N LEU A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 718 through 745 Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 798 through 804 Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 810 through 818 removed outlier: 3.559A pdb=" N ASN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 840 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 848 through 852 removed outlier: 3.652A pdb=" N GLY A 851 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 874 through 881 removed outlier: 4.145A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 903 Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 927 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 938 through 946 Processing helix chain 'A' and resid 950 through 995 removed outlier: 4.088A pdb=" N GLN A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.893A pdb=" N ASN B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.531A pdb=" N ASN B 362 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.678A pdb=" N VAL B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'B' and resid 718 through 745 Processing helix chain 'B' and resid 778 through 787 Processing helix chain 'B' and resid 805 through 809 Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 828 through 840 Processing helix chain 'B' and resid 848 through 852 removed outlier: 3.623A pdb=" N GLY B 851 " --> pdb=" O TRP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 872 Processing helix chain 'B' and resid 874 through 881 removed outlier: 3.961A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 903 removed outlier: 4.129A pdb=" N THR B 901 " --> pdb=" O GLN B 897 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 902 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 927 Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.681A pdb=" N ILE B 942 " --> pdb=" O VAL B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 995 removed outlier: 3.939A pdb=" N VAL B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 278 Processing helix chain 'C' and resid 311 through 317 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.600A pdb=" N LEU C 342 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 4.530A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 715 through 717 No H-bonds generated for 'chain 'C' and resid 715 through 717' Processing helix chain 'C' and resid 718 through 745 removed outlier: 3.555A pdb=" N ASP C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 787 Processing helix chain 'C' and resid 798 through 804 Processing helix chain 'C' and resid 810 through 818 removed outlier: 3.573A pdb=" N ASN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 840 Processing helix chain 'C' and resid 859 through 871 Processing helix chain 'C' and resid 874 through 881 removed outlier: 4.194A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 900 Processing helix chain 'C' and resid 904 through 906 No H-bonds generated for 'chain 'C' and resid 904 through 906' Processing helix chain 'C' and resid 907 through 927 removed outlier: 3.662A pdb=" N LEU C 921 " --> pdb=" O ASN C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 930 No H-bonds generated for 'chain 'C' and resid 928 through 930' Processing helix chain 'C' and resid 938 through 946 Processing helix chain 'C' and resid 950 through 994 removed outlier: 3.874A pdb=" N GLN C 954 " --> pdb=" O GLU C 950 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 removed outlier: 8.279A pdb=" N ASN A 59 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS A 243 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 168 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 167 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR A 185 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.628A pdb=" N GLY A 98 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 94 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG A 93 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 117 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR A 150 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 119 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 148 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 121 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N CYS A 146 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 142 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 288 removed outlier: 3.511A pdb=" N PHE A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 302 removed outlier: 4.462A pdb=" N ASP A 298 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP A 539 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 540 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 332 removed outlier: 4.098A pdb=" N VAL A 369 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.491A pdb=" N CYS A 335 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 489 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AB1, first strand: chain 'A' and resid 446 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 619 through 620 removed outlier: 6.017A pdb=" N GLU A 619 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 658 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 663 through 665 removed outlier: 6.838A pdb=" N ALA A 663 " --> pdb=" O ILE C 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 673 through 690 removed outlier: 6.526A pdb=" N THR A 673 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A1038 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 675 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A1036 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A1034 " --> pdb=" O PRO A 677 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR A1029 " --> pdb=" O HIS A1010 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS A1010 " --> pdb=" O TYR A1029 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 673 through 690 removed outlier: 6.526A pdb=" N THR A 673 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A1038 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 675 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A1036 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A1034 " --> pdb=" O PRO A 677 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1038 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A1040 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A1057 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 698 removed outlier: 4.210A pdb=" N LYS A 695 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB8, first strand: chain 'A' and resid 1048 through 1052 removed outlier: 4.772A pdb=" N ALA A1049 " --> pdb=" O SER A1085 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 24 through 28 removed outlier: 7.834A pdb=" N ASN B 59 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS B 243 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 167 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU B 181 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 212 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 183 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 45 through 53 removed outlier: 3.763A pdb=" N ASP B 261 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.071A pdb=" N ARG B 93 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 117 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.628A pdb=" N HIS B 125 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 285 through 288 Processing sheet with id=AC5, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.192A pdb=" N ASP B 298 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP B 539 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 540 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 328 through 332 removed outlier: 3.969A pdb=" N VAL B 369 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 489 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS B 335 " --> pdb=" O CYS B 490 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 328 through 332 removed outlier: 3.969A pdb=" N VAL B 369 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN B 368 " --> pdb=" O GLU B 481 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 481 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 426 through 428 Processing sheet with id=AC9, first strand: chain 'B' and resid 446 through 449 Processing sheet with id=AD1, first strand: chain 'B' and resid 619 through 620 removed outlier: 6.068A pdb=" N GLU B 619 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL B 658 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 673 through 690 removed outlier: 6.443A pdb=" N THR B 673 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1038 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 675 " --> pdb=" O ASN B1036 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASN B1036 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU B1034 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B1029 " --> pdb=" O HIS B1010 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS B1010 " --> pdb=" O TYR B1029 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 673 through 690 removed outlier: 6.443A pdb=" N THR B 673 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1038 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 675 " --> pdb=" O ASN B1036 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASN B1036 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU B1034 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B1040 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B1057 " --> pdb=" O ALA B1040 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 695 through 698 removed outlier: 4.408A pdb=" N LYS B 695 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD6, first strand: chain 'B' and resid 758 through 759 Processing sheet with id=AD7, first strand: chain 'B' and resid 1048 through 1052 removed outlier: 4.708A pdb=" N ALA B1049 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 24 through 28 removed outlier: 7.609A pdb=" N ASN C 59 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N HIS C 243 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 167 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU C 181 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS C 212 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 183 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AE2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.552A pdb=" N GLY C 94 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 93 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 117 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR C 123 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS C 146 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS C 125 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE C 144 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS C 127 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N SER C 142 " --> pdb=" O CYS C 127 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N THR C 129 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N TYR C 140 " --> pdb=" O THR C 129 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 285 through 288 Processing sheet with id=AE4, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.238A pdb=" N ASP C 298 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASP C 539 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 540 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 328 through 332 removed outlier: 3.999A pdb=" N VAL C 369 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 489 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS C 335 " --> pdb=" O CYS C 490 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 328 through 332 removed outlier: 3.999A pdb=" N VAL C 369 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN C 368 " --> pdb=" O GLU C 481 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU C 481 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 426 through 428 Processing sheet with id=AE8, first strand: chain 'C' and resid 446 through 449 Processing sheet with id=AE9, first strand: chain 'C' and resid 619 through 620 removed outlier: 6.588A pdb=" N ILE C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 673 through 690 removed outlier: 6.430A pdb=" N THR C 673 " --> pdb=" O THR C1038 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C1038 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 675 " --> pdb=" O ASN C1036 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN C1036 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1034 " --> pdb=" O PRO C 677 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR C1029 " --> pdb=" O HIS C1010 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS C1010 " --> pdb=" O TYR C1029 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 673 through 690 removed outlier: 6.430A pdb=" N THR C 673 " --> pdb=" O THR C1038 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C1038 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 675 " --> pdb=" O ASN C1036 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN C1036 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1034 " --> pdb=" O PRO C 677 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C1038 " --> pdb=" O SER C1059 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C1040 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE C1057 " --> pdb=" O ALA C1040 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 695 through 698 removed outlier: 4.215A pdb=" N LYS C 695 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 758 through 759 Processing sheet with id=AF5, first strand: chain 'C' and resid 1048 through 1052 removed outlier: 4.710A pdb=" N ALA C1049 " --> pdb=" O SER C1085 " (cutoff:3.500A) 1081 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7550 1.34 - 1.47: 7543 1.47 - 1.60: 11324 1.60 - 1.73: 0 1.73 - 1.86: 153 Bond restraints: 26570 Sorted by residual: bond pdb=" C12 EIC B1301 " pdb=" C13 EIC B1301 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C12 EIC A1313 " pdb=" C13 EIC A1313 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C12 EIC C1301 " pdb=" C13 EIC C1301 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C10 EIC B1301 " pdb=" C9 EIC B1301 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.31e+01 ... (remaining 26565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 35925 3.14 - 6.29: 192 6.29 - 9.43: 36 9.43 - 12.57: 2 12.57 - 15.72: 12 Bond angle restraints: 36167 Sorted by residual: angle pdb=" C12 EIC B1301 " pdb=" C13 EIC B1301 " pdb=" C14 EIC B1301 " ideal model delta sigma weight residual 128.16 112.44 15.72 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C11 EIC C1301 " pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 127.32 111.64 15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" C11 EIC A1313 " pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " ideal model delta sigma weight residual 127.32 111.79 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C11 EIC C1301 " pdb=" C12 EIC C1301 " pdb=" C13 EIC C1301 " ideal model delta sigma weight residual 127.66 112.18 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C10 EIC B1301 " pdb=" C9 EIC B1301 " pdb=" C8 EIC B1301 " ideal model delta sigma weight residual 127.75 112.30 15.45 3.00e+00 1.11e-01 2.65e+01 ... (remaining 36162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14786 17.98 - 35.97: 1397 35.97 - 53.95: 342 53.95 - 71.94: 84 71.94 - 89.92: 34 Dihedral angle restraints: 16643 sinusoidal: 7349 harmonic: 9294 Sorted by residual: dihedral pdb=" CB CYS A 503 " pdb=" SG CYS A 503 " pdb=" SG CYS A 555 " pdb=" CB CYS A 555 " ideal model delta sinusoidal sigma weight residual 93.00 6.42 86.58 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 122 " pdb=" SG CYS B 122 " pdb=" SG CYS B 146 " pdb=" CB CYS B 146 " ideal model delta sinusoidal sigma weight residual -86.00 -21.25 -64.75 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS C 122 " pdb=" SG CYS C 122 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual -86.00 -31.30 -54.70 1 1.00e+01 1.00e-02 4.05e+01 ... (remaining 16640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4262 0.134 - 0.269: 29 0.269 - 0.403: 0 0.403 - 0.537: 2 0.537 - 0.672: 2 Chirality restraints: 4295 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.34e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 218 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 344 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 4292 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1301 " -0.384 2.00e-02 2.50e+03 2.49e-01 1.55e+03 pdb=" C1A BLA A1301 " 0.298 2.00e-02 2.50e+03 pdb=" C1D BLA A1301 " 0.003 2.00e-02 2.50e+03 pdb=" C2D BLA A1301 " -0.062 2.00e-02 2.50e+03 pdb=" C3D BLA A1301 " 0.009 2.00e-02 2.50e+03 pdb=" C4D BLA A1301 " -0.220 2.00e-02 2.50e+03 pdb=" CAD BLA A1301 " 0.315 2.00e-02 2.50e+03 pdb=" CHA BLA A1301 " -0.203 2.00e-02 2.50e+03 pdb=" CHD BLA A1301 " 0.405 2.00e-02 2.50e+03 pdb=" CMD BLA A1301 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1302 " -0.363 2.00e-02 2.50e+03 2.42e-01 1.46e+03 pdb=" C1A BLA C1302 " 0.268 2.00e-02 2.50e+03 pdb=" C1D BLA C1302 " 0.006 2.00e-02 2.50e+03 pdb=" C2D BLA C1302 " -0.066 2.00e-02 2.50e+03 pdb=" C3D BLA C1302 " 0.013 2.00e-02 2.50e+03 pdb=" C4D BLA C1302 " -0.208 2.00e-02 2.50e+03 pdb=" CAD BLA C1302 " 0.322 2.00e-02 2.50e+03 pdb=" CHA BLA C1302 " -0.193 2.00e-02 2.50e+03 pdb=" CHD BLA C1302 " 0.401 2.00e-02 2.50e+03 pdb=" CMD BLA C1302 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1302 " -0.329 2.00e-02 2.50e+03 2.18e-01 1.18e+03 pdb=" C1A BLA B1302 " 0.236 2.00e-02 2.50e+03 pdb=" C1D BLA B1302 " 0.007 2.00e-02 2.50e+03 pdb=" C2D BLA B1302 " -0.059 2.00e-02 2.50e+03 pdb=" C3D BLA B1302 " 0.022 2.00e-02 2.50e+03 pdb=" C4D BLA B1302 " -0.181 2.00e-02 2.50e+03 pdb=" CAD BLA B1302 " 0.287 2.00e-02 2.50e+03 pdb=" CHA BLA B1302 " -0.174 2.00e-02 2.50e+03 pdb=" CHD BLA B1302 " 0.361 2.00e-02 2.50e+03 pdb=" CMD BLA B1302 " -0.170 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7451 2.81 - 3.33: 21654 3.33 - 3.86: 45421 3.86 - 4.38: 52500 4.38 - 4.90: 90639 Nonbonded interactions: 217665 Sorted by model distance: nonbonded pdb=" OG SER A 412 " pdb=" OD2 ASP A 416 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 670 " pdb=" OG1 THR B 673 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLU B 380 " pdb=" OH TYR B 460 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU C 380 " pdb=" OH TYR C 460 " model vdw 2.315 3.040 nonbonded pdb=" OG SER B 412 " pdb=" OD2 ASP B 416 " model vdw 2.316 3.040 ... (remaining 217660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 1102 or resid 1303 through 1312)) selection = (chain 'B' and (resid 17 through 1102 or resid 1303 through 1312)) selection = (chain 'C' and (resid 17 through 1102 or resid 1303 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'K' } 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=0.00 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: 1.960 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.340 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.005 0.194 26679 Z= 0.245 Angle : 0.767 19.312 36455 Z= 0.376 Chirality : 0.051 0.672 4295 Planarity : 0.011 0.330 4556 Dihedral : 15.259 89.922 10556 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.99 % Allowed : 16.14 % Favored : 81.87 % 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: -0.88 (0.14), residues: 3159 helix: -0.13 (0.18), residues: 732 sheet: 0.54 (0.19), residues: 702 loop : -1.29 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 278 TYR 0.028 0.002 TYR A 339 PHE 0.016 0.001 PHE C 280 TRP 0.030 0.002 TRP A 848 HIS 0.007 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00491 (26570) covalent geometry : angle 0.72531 (36167) SS BOND : bond 0.00461 ( 39) SS BOND : angle 1.90744 ( 78) hydrogen bonds : bond 0.18483 ( 1035) hydrogen bonds : angle 8.22606 ( 2949) link_ALPHA1-2 : bond 0.00168 ( 1) link_ALPHA1-2 : angle 1.59824 ( 3) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 1.31018 ( 9) link_ALPHA1-6 : bond 0.00621 ( 1) link_ALPHA1-6 : angle 1.19606 ( 3) link_BETA1-4 : bond 0.01245 ( 17) link_BETA1-4 : angle 2.66964 ( 51) link_NAG-ASN : bond 0.00611 ( 48) link_NAG-ASN : angle 3.50349 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8346 (m) REVERT: A 167 LYS cc_start: 0.8311 (mptm) cc_final: 0.7987 (mmtm) REVERT: A 245 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8504 (mttm) REVERT: A 314 GLU cc_start: 0.8646 (mp0) cc_final: 0.8194 (mp0) REVERT: A 494 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.4629 (pt0) REVERT: A 502 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8398 (mtpp) REVERT: A 640 HIS cc_start: 0.7781 (t-90) cc_final: 0.7522 (t-90) REVERT: A 717 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: A 742 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8754 (mt-10) REVERT: A 756 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 807 GLN cc_start: 0.8534 (pm20) cc_final: 0.8225 (pm20) REVERT: A 898 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7865 (tm-30) REVERT: A 964 GLN cc_start: 0.8895 (tp40) cc_final: 0.7891 (tm-30) REVERT: A 981 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.7887 (tpt170) REVERT: A 1007 LYS cc_start: 0.9023 (mppt) cc_final: 0.8756 (tppp) REVERT: A 1076 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (pp) REVERT: B 115 THR cc_start: 0.9168 (p) cc_final: 0.8791 (t) REVERT: B 756 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 883 LYS cc_start: 0.8936 (mttp) cc_final: 0.8705 (mmmm) REVERT: B 964 GLN cc_start: 0.8859 (tp40) cc_final: 0.7789 (tm-30) REVERT: B 972 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: C 167 LYS cc_start: 0.8375 (mmtp) cc_final: 0.8004 (mmtm) REVERT: C 235 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5633 (pp) REVERT: C 314 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8497 (mp0) REVERT: C 382 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.7997 (ptt180) REVERT: C 433 GLU cc_start: 0.7010 (tt0) cc_final: 0.6729 (tt0) REVERT: C 640 HIS cc_start: 0.7921 (t-90) cc_final: 0.7489 (t-90) REVERT: C 756 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8399 (mm) REVERT: C 776 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8381 (mmtt) REVERT: C 964 GLN cc_start: 0.8856 (tp40) cc_final: 0.7854 (tm-30) REVERT: C 979 GLU cc_start: 0.8416 (tp30) cc_final: 0.7961 (tt0) REVERT: C 981 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.7810 (tpt170) REVERT: C 1085 SER cc_start: 0.8977 (m) cc_final: 0.8647 (t) outliers start: 55 outliers final: 30 residues processed: 233 average time/residue: 0.6757 time to fit residues: 182.3826 Evaluate side-chains 214 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 901 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 448 GLN C 470 HIS C 521 ASN C 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.090406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.065549 restraints weight = 38838.782| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.48 r_work: 0.2653 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26679 Z= 0.125 Angle : 0.587 17.479 36455 Z= 0.293 Chirality : 0.047 0.642 4295 Planarity : 0.003 0.036 4556 Dihedral : 7.764 74.120 5086 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.74 % Allowed : 15.02 % Favored : 82.23 % 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: -0.32 (0.14), residues: 3159 helix: 0.78 (0.19), residues: 735 sheet: 0.64 (0.18), residues: 729 loop : -1.07 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 30 TYR 0.022 0.001 TYR B 339 PHE 0.013 0.001 PHE C 172 TRP 0.017 0.001 TRP A 848 HIS 0.003 0.001 HIS C 640 Details of bonding type rmsd covalent geometry : bond 0.00268 (26570) covalent geometry : angle 0.54484 (36167) SS BOND : bond 0.00304 ( 39) SS BOND : angle 1.48729 ( 78) hydrogen bonds : bond 0.04679 ( 1035) hydrogen bonds : angle 6.18566 ( 2949) link_ALPHA1-2 : bond 0.00155 ( 1) link_ALPHA1-2 : angle 1.69556 ( 3) link_ALPHA1-3 : bond 0.00660 ( 3) link_ALPHA1-3 : angle 1.27185 ( 9) link_ALPHA1-6 : bond 0.00661 ( 1) link_ALPHA1-6 : angle 1.29346 ( 3) link_BETA1-4 : bond 0.00401 ( 17) link_BETA1-4 : angle 2.22561 ( 51) link_NAG-ASN : bond 0.00483 ( 48) link_NAG-ASN : angle 3.10939 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7880 (mmtm) REVERT: A 245 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8672 (mttp) REVERT: A 314 GLU cc_start: 0.8651 (mp0) cc_final: 0.8198 (mp0) REVERT: A 494 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.4629 (pt0) REVERT: A 502 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8407 (mtpp) REVERT: A 548 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: A 756 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 807 GLN cc_start: 0.8538 (pm20) cc_final: 0.8218 (pm20) REVERT: A 898 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7836 (tm-30) REVERT: A 964 GLN cc_start: 0.8963 (tp40) cc_final: 0.7983 (tm-30) REVERT: A 981 ARG cc_start: 0.8688 (ttp-110) cc_final: 0.7973 (tpt170) REVERT: A 1007 LYS cc_start: 0.9052 (mppt) cc_final: 0.8810 (tppp) REVERT: A 1076 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 48 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9121 (mp) REVERT: B 115 THR cc_start: 0.9254 (p) cc_final: 0.8906 (t) REVERT: B 883 LYS cc_start: 0.9027 (mttp) cc_final: 0.8805 (mmmm) REVERT: B 897 GLN cc_start: 0.8837 (tt0) cc_final: 0.8441 (mt0) REVERT: B 964 GLN cc_start: 0.8890 (tp40) cc_final: 0.7877 (tm-30) REVERT: B 972 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: C 235 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5866 (pt) REVERT: C 314 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8521 (mp0) REVERT: C 640 HIS cc_start: 0.7928 (t-90) cc_final: 0.7385 (t-170) REVERT: C 756 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 776 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8398 (mmtt) REVERT: C 895 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8388 (mtpt) REVERT: C 964 GLN cc_start: 0.8930 (tp40) cc_final: 0.7985 (tm-30) REVERT: C 979 GLU cc_start: 0.8434 (tp30) cc_final: 0.8029 (tt0) REVERT: C 981 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.7972 (tpt170) REVERT: C 1085 SER cc_start: 0.9017 (m) cc_final: 0.8717 (t) outliers start: 76 outliers final: 23 residues processed: 248 average time/residue: 0.5932 time to fit residues: 172.2359 Evaluate side-chains 201 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 895 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 138 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.086686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.061928 restraints weight = 39070.361| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.44 r_work: 0.2580 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26679 Z= 0.224 Angle : 0.647 18.101 36455 Z= 0.324 Chirality : 0.050 0.676 4295 Planarity : 0.004 0.063 4556 Dihedral : 7.634 78.174 5051 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.03 % Allowed : 14.27 % Favored : 82.70 % 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: -0.23 (0.14), residues: 3159 helix: 1.00 (0.20), residues: 720 sheet: 0.56 (0.18), residues: 729 loop : -0.99 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 382 TYR 0.022 0.002 TYR B1029 PHE 0.014 0.002 PHE C 172 TRP 0.019 0.002 TRP A 848 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00517 (26570) covalent geometry : angle 0.60258 (36167) SS BOND : bond 0.00510 ( 39) SS BOND : angle 2.01535 ( 78) hydrogen bonds : bond 0.05179 ( 1035) hydrogen bonds : angle 6.03505 ( 2949) link_ALPHA1-2 : bond 0.00074 ( 1) link_ALPHA1-2 : angle 1.88597 ( 3) link_ALPHA1-3 : bond 0.00625 ( 3) link_ALPHA1-3 : angle 1.21223 ( 9) link_ALPHA1-6 : bond 0.00557 ( 1) link_ALPHA1-6 : angle 1.49286 ( 3) link_BETA1-4 : bond 0.00373 ( 17) link_BETA1-4 : angle 2.40685 ( 51) link_NAG-ASN : bond 0.00468 ( 48) link_NAG-ASN : angle 3.23200 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 177 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 167 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7883 (mmtm) REVERT: A 245 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8709 (mttp) REVERT: A 314 GLU cc_start: 0.8651 (mp0) cc_final: 0.8208 (mp0) REVERT: A 494 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.4739 (pt0) REVERT: A 502 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8484 (mtpp) REVERT: A 548 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8630 (pp20) REVERT: A 640 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7630 (t-170) REVERT: A 756 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 807 GLN cc_start: 0.8555 (pm20) cc_final: 0.8241 (pm20) REVERT: A 898 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7949 (tm-30) REVERT: A 964 GLN cc_start: 0.8941 (tp40) cc_final: 0.7901 (tm-30) REVERT: A 981 ARG cc_start: 0.8750 (ttp-110) cc_final: 0.8058 (tpt170) REVERT: A 1007 LYS cc_start: 0.9041 (mppt) cc_final: 0.8794 (tppp) REVERT: A 1076 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 48 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9171 (mp) REVERT: B 115 THR cc_start: 0.9210 (p) cc_final: 0.8868 (t) REVERT: B 175 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8795 (ptmm) REVERT: B 756 ILE cc_start: 0.8727 (pp) cc_final: 0.8313 (mm) REVERT: B 830 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: B 883 LYS cc_start: 0.9037 (mttp) cc_final: 0.8817 (mmmm) REVERT: B 964 GLN cc_start: 0.8938 (tp40) cc_final: 0.8419 (tp40) REVERT: B 972 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: C 30 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: C 235 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.5797 (pt) REVERT: C 278 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8125 (tpp80) REVERT: C 314 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8494 (mp0) REVERT: C 433 GLU cc_start: 0.7179 (tt0) cc_final: 0.6890 (tt0) REVERT: C 640 HIS cc_start: 0.7969 (t-90) cc_final: 0.7384 (t-170) REVERT: C 756 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8490 (mm) REVERT: C 776 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8448 (mmtt) REVERT: C 807 GLN cc_start: 0.8611 (pm20) cc_final: 0.8375 (pm20) REVERT: C 895 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: C 964 GLN cc_start: 0.8934 (tp40) cc_final: 0.8043 (tm-30) REVERT: C 979 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: C 981 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8036 (tpt170) REVERT: C 1085 SER cc_start: 0.9063 (m) cc_final: 0.8813 (t) outliers start: 84 outliers final: 42 residues processed: 239 average time/residue: 0.6481 time to fit residues: 178.9125 Evaluate side-chains 231 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 640 HIS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 598 TRP Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1054 GLU Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 107 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 244 optimal weight: 0.0170 chunk 266 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 288 GLN B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.065575 restraints weight = 38640.507| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.48 r_work: 0.2653 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26679 Z= 0.110 Angle : 0.558 16.969 36455 Z= 0.278 Chirality : 0.046 0.626 4295 Planarity : 0.003 0.033 4556 Dihedral : 7.143 75.943 5050 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.53 % Allowed : 14.99 % Favored : 82.48 % 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: -0.18 (0.14), residues: 3159 helix: 1.28 (0.20), residues: 699 sheet: 0.50 (0.19), residues: 657 loop : -0.95 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.020 0.001 TYR A 339 PHE 0.013 0.001 PHE B 608 TRP 0.018 0.001 TRP A 848 HIS 0.002 0.000 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00232 (26570) covalent geometry : angle 0.51431 (36167) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.64079 ( 78) hydrogen bonds : bond 0.04043 ( 1035) hydrogen bonds : angle 5.67011 ( 2949) link_ALPHA1-2 : bond 0.00242 ( 1) link_ALPHA1-2 : angle 1.65064 ( 3) link_ALPHA1-3 : bond 0.00776 ( 3) link_ALPHA1-3 : angle 1.25595 ( 9) link_ALPHA1-6 : bond 0.00680 ( 1) link_ALPHA1-6 : angle 1.36470 ( 3) link_BETA1-4 : bond 0.00441 ( 17) link_BETA1-4 : angle 2.09644 ( 51) link_NAG-ASN : bond 0.00485 ( 48) link_NAG-ASN : angle 3.03170 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7858 (mmtm) REVERT: A 245 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8626 (mttm) REVERT: A 314 GLU cc_start: 0.8613 (mp0) cc_final: 0.8175 (mp0) REVERT: A 494 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.4429 (pt0) REVERT: A 502 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8409 (mtpp) REVERT: A 548 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: A 640 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7569 (t-170) REVERT: A 756 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 807 GLN cc_start: 0.8541 (pm20) cc_final: 0.8229 (pm20) REVERT: A 898 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7912 (tm-30) REVERT: A 964 GLN cc_start: 0.8974 (tp40) cc_final: 0.8003 (tm-30) REVERT: A 981 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8000 (tpt170) REVERT: A 1007 LYS cc_start: 0.9022 (mppt) cc_final: 0.8782 (tppp) REVERT: A 1076 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8878 (pp) REVERT: B 48 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9168 (mp) REVERT: B 115 THR cc_start: 0.9213 (p) cc_final: 0.8877 (t) REVERT: B 175 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8703 (ptmm) REVERT: B 756 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 830 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: B 875 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.9008 (pt0) REVERT: B 883 LYS cc_start: 0.9010 (mttp) cc_final: 0.8786 (mmmm) REVERT: B 964 GLN cc_start: 0.8913 (tp40) cc_final: 0.7918 (tm-30) REVERT: B 972 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: C 235 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6237 (pt) REVERT: C 314 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8470 (mp0) REVERT: C 640 HIS cc_start: 0.7852 (t-90) cc_final: 0.7335 (t-170) REVERT: C 756 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8413 (mm) REVERT: C 776 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8373 (mmtt) REVERT: C 787 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8730 (mmtm) REVERT: C 807 GLN cc_start: 0.8610 (pm20) cc_final: 0.8368 (pm20) REVERT: C 895 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: C 964 GLN cc_start: 0.8922 (tp40) cc_final: 0.7989 (tm-30) REVERT: C 979 GLU cc_start: 0.8427 (tp30) cc_final: 0.8015 (tt0) REVERT: C 981 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.7968 (tpt170) REVERT: C 1085 SER cc_start: 0.8930 (m) cc_final: 0.8725 (t) outliers start: 70 outliers final: 32 residues processed: 237 average time/residue: 0.6448 time to fit residues: 176.3299 Evaluate side-chains 225 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 640 HIS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 875 GLN Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 217 optimal weight: 0.4980 chunk 168 optimal weight: 0.0020 chunk 292 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 GLN A 651 ASN B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.061830 restraints weight = 38823.785| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.44 r_work: 0.2576 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26679 Z= 0.223 Angle : 0.639 17.752 36455 Z= 0.321 Chirality : 0.050 0.661 4295 Planarity : 0.004 0.063 4556 Dihedral : 7.454 78.313 5045 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.03 % Allowed : 14.37 % Favored : 82.59 % 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: -0.14 (0.14), residues: 3159 helix: 1.21 (0.20), residues: 699 sheet: 0.48 (0.18), residues: 729 loop : -0.90 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.022 0.002 TYR B1029 PHE 0.014 0.002 PHE A 124 TRP 0.021 0.002 TRP A 848 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00518 (26570) covalent geometry : angle 0.59336 (36167) SS BOND : bond 0.00546 ( 39) SS BOND : angle 2.19635 ( 78) hydrogen bonds : bond 0.04971 ( 1035) hydrogen bonds : angle 5.84487 ( 2949) link_ALPHA1-2 : bond 0.00061 ( 1) link_ALPHA1-2 : angle 1.86719 ( 3) link_ALPHA1-3 : bond 0.00609 ( 3) link_ALPHA1-3 : angle 1.22861 ( 9) link_ALPHA1-6 : bond 0.00516 ( 1) link_ALPHA1-6 : angle 1.56626 ( 3) link_BETA1-4 : bond 0.00353 ( 17) link_BETA1-4 : angle 2.37423 ( 51) link_NAG-ASN : bond 0.00446 ( 48) link_NAG-ASN : angle 3.17904 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 177 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 167 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7894 (mmtm) REVERT: A 245 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8695 (mttp) REVERT: A 314 GLU cc_start: 0.8624 (mp0) cc_final: 0.8177 (mp0) REVERT: A 494 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.4706 (pt0) REVERT: A 502 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8494 (mtpp) REVERT: A 548 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: A 640 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7594 (t-170) REVERT: A 651 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7286 (p0) REVERT: A 756 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 807 GLN cc_start: 0.8544 (pm20) cc_final: 0.8225 (pm20) REVERT: A 964 GLN cc_start: 0.8982 (tp40) cc_final: 0.7893 (tm-30) REVERT: A 981 ARG cc_start: 0.8729 (ttp-110) cc_final: 0.8026 (ttt90) REVERT: A 1007 LYS cc_start: 0.9003 (mppt) cc_final: 0.8765 (tppp) REVERT: A 1076 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8936 (pp) REVERT: B 48 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9204 (mp) REVERT: B 115 THR cc_start: 0.9195 (p) cc_final: 0.8849 (t) REVERT: B 175 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8787 (ptmm) REVERT: B 249 MET cc_start: 0.9277 (mtt) cc_final: 0.9000 (mtt) REVERT: B 494 GLN cc_start: 0.8774 (tt0) cc_final: 0.8454 (mt0) REVERT: B 756 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 830 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 883 LYS cc_start: 0.9045 (mttp) cc_final: 0.8826 (mmmm) REVERT: B 964 GLN cc_start: 0.8933 (tp40) cc_final: 0.7922 (tm-30) REVERT: B 972 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8547 (mp10) REVERT: C 235 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6415 (pt) REVERT: C 278 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8192 (tpp80) REVERT: C 314 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8485 (mp0) REVERT: C 433 GLU cc_start: 0.7204 (tt0) cc_final: 0.6910 (tt0) REVERT: C 640 HIS cc_start: 0.7949 (t-90) cc_final: 0.7393 (t-170) REVERT: C 756 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8459 (mm) REVERT: C 776 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8461 (mmtt) REVERT: C 807 GLN cc_start: 0.8582 (pm20) cc_final: 0.8326 (pm20) REVERT: C 895 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: C 964 GLN cc_start: 0.8944 (tp40) cc_final: 0.7955 (tm-30) REVERT: C 979 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: C 981 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8024 (tpt170) REVERT: C 1085 SER cc_start: 0.9004 (m) cc_final: 0.8790 (t) outliers start: 84 outliers final: 46 residues processed: 239 average time/residue: 0.6518 time to fit residues: 179.5112 Evaluate side-chains 229 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 165 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 640 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 448 GLN B 888 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.063209 restraints weight = 38332.885| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.47 r_work: 0.2600 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26679 Z= 0.155 Angle : 0.596 17.329 36455 Z= 0.299 Chirality : 0.048 0.641 4295 Planarity : 0.003 0.036 4556 Dihedral : 7.272 77.700 5043 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.00 % Allowed : 14.73 % Favored : 82.27 % 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: -0.12 (0.14), residues: 3159 helix: 1.25 (0.20), residues: 696 sheet: 0.46 (0.18), residues: 729 loop : -0.89 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.019 0.001 TYR C1029 PHE 0.011 0.001 PHE B 608 TRP 0.023 0.002 TRP A 848 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00350 (26570) covalent geometry : angle 0.54839 (36167) SS BOND : bond 0.00395 ( 39) SS BOND : angle 1.98646 ( 78) hydrogen bonds : bond 0.04468 ( 1035) hydrogen bonds : angle 5.70934 ( 2949) link_ALPHA1-2 : bond 0.00091 ( 1) link_ALPHA1-2 : angle 1.74855 ( 3) link_ALPHA1-3 : bond 0.00700 ( 3) link_ALPHA1-3 : angle 1.20683 ( 9) link_ALPHA1-6 : bond 0.00618 ( 1) link_ALPHA1-6 : angle 1.33261 ( 3) link_BETA1-4 : bond 0.00346 ( 17) link_BETA1-4 : angle 2.23270 ( 51) link_NAG-ASN : bond 0.00454 ( 48) link_NAG-ASN : angle 3.22257 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 177 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7841 (mmtm) REVERT: A 245 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8665 (mttp) REVERT: A 314 GLU cc_start: 0.8585 (mp0) cc_final: 0.8122 (mp0) REVERT: A 494 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.4623 (pt0) REVERT: A 502 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8454 (mtpp) REVERT: A 548 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8577 (pp20) REVERT: A 640 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7510 (t-170) REVERT: A 756 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8420 (mm) REVERT: A 807 GLN cc_start: 0.8539 (pm20) cc_final: 0.8218 (pm20) REVERT: A 964 GLN cc_start: 0.8921 (tp40) cc_final: 0.7847 (tm-30) REVERT: A 981 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.7988 (tpt170) REVERT: A 1007 LYS cc_start: 0.8969 (tppt) cc_final: 0.8729 (tppp) REVERT: A 1076 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8866 (pp) REVERT: B 48 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9189 (mp) REVERT: B 115 THR cc_start: 0.9171 (p) cc_final: 0.8822 (t) REVERT: B 175 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8736 (ptmm) REVERT: B 249 MET cc_start: 0.9263 (mtt) cc_final: 0.8974 (mtt) REVERT: B 494 GLN cc_start: 0.8726 (tt0) cc_final: 0.8371 (mt0) REVERT: B 756 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 830 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: B 883 LYS cc_start: 0.9025 (mttp) cc_final: 0.8789 (mmmm) REVERT: B 964 GLN cc_start: 0.8900 (tp40) cc_final: 0.7878 (tm-30) REVERT: B 972 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8440 (mp10) REVERT: C 235 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.5785 (pp) REVERT: C 278 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8111 (tpp80) REVERT: C 314 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8448 (mp0) REVERT: C 433 GLU cc_start: 0.7096 (tt0) cc_final: 0.6791 (tt0) REVERT: C 640 HIS cc_start: 0.7909 (t-90) cc_final: 0.7347 (t-170) REVERT: C 756 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8443 (mm) REVERT: C 776 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8470 (mmtt) REVERT: C 807 GLN cc_start: 0.8597 (pm20) cc_final: 0.8337 (pm20) REVERT: C 895 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8399 (mtpt) REVERT: C 964 GLN cc_start: 0.8893 (tp40) cc_final: 0.7905 (tm-30) REVERT: C 979 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: C 981 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.7940 (tpt170) outliers start: 83 outliers final: 50 residues processed: 244 average time/residue: 0.6300 time to fit residues: 178.1765 Evaluate side-chains 236 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 640 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 752 LYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 62 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 243 optimal weight: 0.4980 chunk 275 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.063922 restraints weight = 38345.392| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.49 r_work: 0.2618 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26679 Z= 0.128 Angle : 0.576 17.155 36455 Z= 0.288 Chirality : 0.047 0.628 4295 Planarity : 0.003 0.033 4556 Dihedral : 7.186 76.975 5043 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.93 % Allowed : 14.70 % Favored : 82.38 % 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: -0.15 (0.14), residues: 3159 helix: 1.32 (0.20), residues: 696 sheet: 0.42 (0.19), residues: 657 loop : -0.89 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 278 TYR 0.019 0.001 TYR A 339 PHE 0.011 0.001 PHE C 124 TRP 0.025 0.001 TRP A 848 HIS 0.002 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00284 (26570) covalent geometry : angle 0.53140 (36167) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.72557 ( 78) hydrogen bonds : bond 0.04227 ( 1035) hydrogen bonds : angle 5.61243 ( 2949) link_ALPHA1-2 : bond 0.00155 ( 1) link_ALPHA1-2 : angle 1.71605 ( 3) link_ALPHA1-3 : bond 0.00689 ( 3) link_ALPHA1-3 : angle 1.22528 ( 9) link_ALPHA1-6 : bond 0.00601 ( 1) link_ALPHA1-6 : angle 1.33987 ( 3) link_BETA1-4 : bond 0.00353 ( 17) link_BETA1-4 : angle 2.17296 ( 51) link_NAG-ASN : bond 0.00474 ( 48) link_NAG-ASN : angle 3.09800 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.8770 (t) cc_final: 0.8550 (m) REVERT: A 245 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8677 (mttp) REVERT: A 494 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.4512 (pt0) REVERT: A 502 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8448 (mtpp) REVERT: A 548 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: A 611 GLN cc_start: 0.8720 (tt0) cc_final: 0.8246 (tp40) REVERT: A 640 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7534 (t-170) REVERT: A 756 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 807 GLN cc_start: 0.8539 (pm20) cc_final: 0.8220 (pm20) REVERT: A 964 GLN cc_start: 0.8943 (tp40) cc_final: 0.7925 (tm-30) REVERT: A 981 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.7946 (tpt170) REVERT: A 1007 LYS cc_start: 0.8961 (tppt) cc_final: 0.8740 (tppp) REVERT: A 1076 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 48 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9184 (mp) REVERT: B 115 THR cc_start: 0.9178 (p) cc_final: 0.8831 (t) REVERT: B 175 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8702 (ptmm) REVERT: B 249 MET cc_start: 0.9270 (mtt) cc_final: 0.8994 (mtt) REVERT: B 494 GLN cc_start: 0.8729 (tt0) cc_final: 0.8351 (mt0) REVERT: B 830 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: B 883 LYS cc_start: 0.9033 (mttp) cc_final: 0.8802 (mmmm) REVERT: B 964 GLN cc_start: 0.8891 (tp40) cc_final: 0.7839 (tm-30) REVERT: B 972 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: C 235 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6395 (pt) REVERT: C 278 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8147 (tpp80) REVERT: C 314 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8453 (mp0) REVERT: C 433 GLU cc_start: 0.7093 (tt0) cc_final: 0.6749 (tt0) REVERT: C 640 HIS cc_start: 0.7872 (t-90) cc_final: 0.7294 (t-170) REVERT: C 756 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8460 (mm) REVERT: C 776 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8445 (mmtt) REVERT: C 807 GLN cc_start: 0.8634 (pm20) cc_final: 0.8377 (pm20) REVERT: C 895 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (mtpt) REVERT: C 964 GLN cc_start: 0.8906 (tp40) cc_final: 0.7947 (tm-30) REVERT: C 979 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: C 981 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.7961 (tpt170) outliers start: 81 outliers final: 48 residues processed: 240 average time/residue: 0.6402 time to fit residues: 177.8378 Evaluate side-chains 231 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 640 HIS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 752 LYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 190 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1045 HIS B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.061842 restraints weight = 38645.907| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.49 r_work: 0.2571 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26679 Z= 0.210 Angle : 0.633 17.544 36455 Z= 0.319 Chirality : 0.050 0.654 4295 Planarity : 0.004 0.058 4556 Dihedral : 7.416 78.522 5043 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.93 % Allowed : 14.81 % Favored : 82.27 % 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: -0.13 (0.14), residues: 3159 helix: 1.24 (0.20), residues: 696 sheet: 0.45 (0.18), residues: 729 loop : -0.88 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.021 0.002 TYR A1029 PHE 0.013 0.001 PHE A 172 TRP 0.028 0.002 TRP A 848 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00489 (26570) covalent geometry : angle 0.58687 (36167) SS BOND : bond 0.00501 ( 39) SS BOND : angle 2.12745 ( 78) hydrogen bonds : bond 0.04833 ( 1035) hydrogen bonds : angle 5.76890 ( 2949) link_ALPHA1-2 : bond 0.00039 ( 1) link_ALPHA1-2 : angle 1.82998 ( 3) link_ALPHA1-3 : bond 0.00625 ( 3) link_ALPHA1-3 : angle 1.21402 ( 9) link_ALPHA1-6 : bond 0.00510 ( 1) link_ALPHA1-6 : angle 1.50984 ( 3) link_BETA1-4 : bond 0.00309 ( 17) link_BETA1-4 : angle 2.36720 ( 51) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 3.18692 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8692 (mttp) REVERT: A 494 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.4697 (pt0) REVERT: A 502 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8492 (mtpp) REVERT: A 548 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8687 (pp20) REVERT: A 756 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 807 GLN cc_start: 0.8555 (pm20) cc_final: 0.8230 (pm20) REVERT: A 964 GLN cc_start: 0.8951 (tp40) cc_final: 0.7850 (tm-30) REVERT: A 981 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.7985 (ttt90) REVERT: A 1007 LYS cc_start: 0.8946 (tppt) cc_final: 0.8725 (tppp) REVERT: A 1076 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 48 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9192 (mp) REVERT: B 115 THR cc_start: 0.9171 (p) cc_final: 0.8819 (t) REVERT: B 175 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8713 (ptmm) REVERT: B 494 GLN cc_start: 0.8758 (tt0) cc_final: 0.8427 (mt0) REVERT: B 830 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: B 883 LYS cc_start: 0.9052 (mttp) cc_final: 0.8825 (mmmm) REVERT: B 897 GLN cc_start: 0.8822 (tt0) cc_final: 0.8316 (mt0) REVERT: B 964 GLN cc_start: 0.8918 (tp40) cc_final: 0.7891 (tm-30) REVERT: B 972 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: C 235 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6177 (pt) REVERT: C 278 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8256 (tpp80) REVERT: C 314 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8456 (mp0) REVERT: C 433 GLU cc_start: 0.7173 (tt0) cc_final: 0.6876 (tt0) REVERT: C 640 HIS cc_start: 0.7842 (t-90) cc_final: 0.7391 (t-170) REVERT: C 756 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 776 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8469 (mmtt) REVERT: C 807 GLN cc_start: 0.8591 (pm20) cc_final: 0.8217 (pm20) REVERT: C 895 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: C 964 GLN cc_start: 0.8918 (tp40) cc_final: 0.7919 (tm-30) REVERT: C 979 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: C 981 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8000 (tpt170) outliers start: 81 outliers final: 49 residues processed: 237 average time/residue: 0.6151 time to fit residues: 168.7225 Evaluate side-chains 231 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 210 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 303 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 192 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN C 297 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.065694 restraints weight = 38432.393| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.50 r_work: 0.2652 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26679 Z= 0.106 Angle : 0.562 16.820 36455 Z= 0.282 Chirality : 0.046 0.604 4295 Planarity : 0.003 0.033 4556 Dihedral : 7.027 76.405 5043 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 15.78 % Favored : 82.16 % 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: -0.14 (0.14), residues: 3159 helix: 1.38 (0.20), residues: 696 sheet: 0.43 (0.19), residues: 642 loop : -0.89 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 156 TYR 0.019 0.001 TYR A 339 PHE 0.019 0.001 PHE A 124 TRP 0.033 0.002 TRP A 848 HIS 0.002 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00225 (26570) covalent geometry : angle 0.52000 (36167) SS BOND : bond 0.00511 ( 39) SS BOND : angle 1.66783 ( 78) hydrogen bonds : bond 0.03892 ( 1035) hydrogen bonds : angle 5.49878 ( 2949) link_ALPHA1-2 : bond 0.00265 ( 1) link_ALPHA1-2 : angle 1.62444 ( 3) link_ALPHA1-3 : bond 0.00772 ( 3) link_ALPHA1-3 : angle 1.25105 ( 9) link_ALPHA1-6 : bond 0.00656 ( 1) link_ALPHA1-6 : angle 1.30310 ( 3) link_BETA1-4 : bond 0.00409 ( 17) link_BETA1-4 : angle 2.04893 ( 51) link_NAG-ASN : bond 0.00497 ( 48) link_NAG-ASN : angle 2.99648 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.8759 (t) cc_final: 0.8556 (m) REVERT: A 245 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8648 (mttp) REVERT: A 494 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.4376 (pt0) REVERT: A 502 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8412 (mtpp) REVERT: A 548 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8447 (pp20) REVERT: A 611 GLN cc_start: 0.8591 (mt0) cc_final: 0.8120 (tp40) REVERT: A 756 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 807 GLN cc_start: 0.8535 (pm20) cc_final: 0.8222 (pm20) REVERT: A 964 GLN cc_start: 0.8949 (tp40) cc_final: 0.7937 (tm-30) REVERT: A 981 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.7977 (tpt170) REVERT: A 1007 LYS cc_start: 0.8942 (tppt) cc_final: 0.8733 (tppp) REVERT: A 1076 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 48 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9158 (mp) REVERT: B 115 THR cc_start: 0.9165 (p) cc_final: 0.8828 (t) REVERT: B 175 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8581 (ptmm) REVERT: B 494 GLN cc_start: 0.8719 (tt0) cc_final: 0.8345 (mt0) REVERT: B 830 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: B 883 LYS cc_start: 0.9011 (mttp) cc_final: 0.8782 (mmmm) REVERT: B 897 GLN cc_start: 0.8780 (tt0) cc_final: 0.8316 (mt0) REVERT: B 964 GLN cc_start: 0.8897 (tp40) cc_final: 0.7852 (tm-30) REVERT: B 972 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: C 235 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.5906 (pp) REVERT: C 314 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8419 (mp0) REVERT: C 433 GLU cc_start: 0.7163 (tt0) cc_final: 0.6795 (tt0) REVERT: C 640 HIS cc_start: 0.7853 (t-90) cc_final: 0.7311 (t-170) REVERT: C 756 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8391 (mm) REVERT: C 776 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8465 (mmtt) REVERT: C 807 GLN cc_start: 0.8621 (pm20) cc_final: 0.8364 (pm20) REVERT: C 895 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8397 (mtpt) REVERT: C 964 GLN cc_start: 0.8878 (tp40) cc_final: 0.7917 (tm-30) REVERT: C 979 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: C 981 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.7925 (tpt170) outliers start: 57 outliers final: 34 residues processed: 228 average time/residue: 0.6798 time to fit residues: 178.9225 Evaluate side-chains 222 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 895 LYS Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 448 GLN C 521 ASN C 863 GLN C 917 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.064569 restraints weight = 38392.579| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.48 r_work: 0.2632 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26679 Z= 0.134 Angle : 0.588 16.969 36455 Z= 0.296 Chirality : 0.047 0.613 4295 Planarity : 0.003 0.035 4556 Dihedral : 6.997 76.179 5043 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.84 % Allowed : 16.00 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3159 helix: 1.41 (0.20), residues: 696 sheet: 0.44 (0.19), residues: 657 loop : -0.88 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.019 0.001 TYR B 339 PHE 0.014 0.001 PHE A 721 TRP 0.036 0.002 TRP A 848 HIS 0.002 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00303 (26570) covalent geometry : angle 0.54401 (36167) SS BOND : bond 0.00355 ( 39) SS BOND : angle 2.05397 ( 78) hydrogen bonds : bond 0.04123 ( 1035) hydrogen bonds : angle 5.52276 ( 2949) link_ALPHA1-2 : bond 0.00145 ( 1) link_ALPHA1-2 : angle 1.70005 ( 3) link_ALPHA1-3 : bond 0.00619 ( 3) link_ALPHA1-3 : angle 1.22731 ( 9) link_ALPHA1-6 : bond 0.00552 ( 1) link_ALPHA1-6 : angle 1.37748 ( 3) link_BETA1-4 : bond 0.00342 ( 17) link_BETA1-4 : angle 2.13159 ( 51) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 3.01019 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8665 (mttp) REVERT: A 494 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.4431 (pt0) REVERT: A 502 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8453 (mtpp) REVERT: A 548 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8524 (pp20) REVERT: A 611 GLN cc_start: 0.8658 (mt0) cc_final: 0.8209 (tp40) REVERT: A 756 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 807 GLN cc_start: 0.8549 (pm20) cc_final: 0.8235 (pm20) REVERT: A 964 GLN cc_start: 0.8950 (tp40) cc_final: 0.7938 (tm-30) REVERT: A 981 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.7951 (tpt170) REVERT: A 1076 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 48 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9172 (mp) REVERT: B 115 THR cc_start: 0.9169 (p) cc_final: 0.8822 (t) REVERT: B 175 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8679 (ptmm) REVERT: B 494 GLN cc_start: 0.8742 (tt0) cc_final: 0.8377 (mt0) REVERT: B 830 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: B 883 LYS cc_start: 0.9017 (mttp) cc_final: 0.8791 (mmmm) REVERT: B 964 GLN cc_start: 0.8899 (tp40) cc_final: 0.7860 (tm-30) REVERT: B 972 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: C 235 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.5842 (pp) REVERT: C 314 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8425 (mp0) REVERT: C 433 GLU cc_start: 0.7158 (tt0) cc_final: 0.6853 (tt0) REVERT: C 640 HIS cc_start: 0.7903 (t-90) cc_final: 0.7356 (t-170) REVERT: C 756 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 776 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8449 (mmtt) REVERT: C 807 GLN cc_start: 0.8621 (pm20) cc_final: 0.8362 (pm20) REVERT: C 964 GLN cc_start: 0.8903 (tp40) cc_final: 0.7954 (tm-30) REVERT: C 979 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: C 981 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.7967 (tpt170) outliers start: 51 outliers final: 32 residues processed: 219 average time/residue: 0.7013 time to fit residues: 176.7153 Evaluate side-chains 218 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 972 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 979 GLU Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1087 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN C 521 ASN C 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.089746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.064690 restraints weight = 38403.485| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.49 r_work: 0.2625 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26679 Z= 0.138 Angle : 0.595 16.948 36455 Z= 0.298 Chirality : 0.047 0.613 4295 Planarity : 0.003 0.033 4556 Dihedral : 6.955 76.249 5041 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.17 % Allowed : 15.60 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3159 helix: 1.42 (0.20), residues: 696 sheet: 0.44 (0.19), residues: 657 loop : -0.87 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.019 0.001 TYR B 339 PHE 0.014 0.001 PHE A 124 TRP 0.038 0.002 TRP A 848 HIS 0.002 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00316 (26570) covalent geometry : angle 0.54860 (36167) SS BOND : bond 0.00391 ( 39) SS BOND : angle 2.36143 ( 78) hydrogen bonds : bond 0.04112 ( 1035) hydrogen bonds : angle 5.52424 ( 2949) link_ALPHA1-2 : bond 0.00142 ( 1) link_ALPHA1-2 : angle 1.69166 ( 3) link_ALPHA1-3 : bond 0.00649 ( 3) link_ALPHA1-3 : angle 1.21643 ( 9) link_ALPHA1-6 : bond 0.00576 ( 1) link_ALPHA1-6 : angle 1.32491 ( 3) link_BETA1-4 : bond 0.00350 ( 17) link_BETA1-4 : angle 2.12562 ( 51) link_NAG-ASN : bond 0.00461 ( 48) link_NAG-ASN : angle 3.03917 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10074.86 seconds wall clock time: 172 minutes 0.74 seconds (10320.74 seconds total)