Starting phenix.real_space_refine on Sat Jul 4 19:21:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmp_38485/07_2026/8xmp_38485_neut.cif" } resolution = 3.11 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= 0.040 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: 6 Type Number sf(0) Gaussians Ca 23 9.91 5 Fe 2 7.16 5 S 218 5.16 5 C 14198 2.51 5 N 4085 2.21 5 O 4423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22949 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5455 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain breaks: 5 Chain: "F" Number of atoms: 6370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6370 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "D" Number of atoms: 6369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6369 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "C" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "Y" 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: 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: "X" 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: "2" 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 28 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 5 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 42 Ad-hoc single atom residues: {' CA': 9} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 42 Ad-hoc single atom residues: {' CA': 9} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.21 Number of scatterers: 22949 At special positions: 0 Unit cell: (138.03, 135.89, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 23 19.99 S 218 16.00 O 4423 8.00 N 4085 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 355 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 335 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 411 " - pdb=" SG CYS E 472 " distance=2.03 Simple disulfide: pdb=" SG CYS E 442 " - pdb=" SG CYS E 452 " distance=2.03 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.03 Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.03 Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03 Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.03 Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03 Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.03 Simple disulfide: pdb=" SG CYS E 938 " - pdb=" SG CYS E 972 " distance=2.03 Simple disulfide: pdb=" SG CYS E 954 " - pdb=" SG CYS E1018 " distance=2.03 Simple disulfide: pdb=" SG CYS E 967 " - pdb=" SG CYS E1028 " distance=2.03 Simple disulfide: pdb=" SG CYS E 998 " - pdb=" SG CYS E1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 258 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 335 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 472 " distance=2.03 Simple disulfide: pdb=" SG CYS F 442 " - pdb=" SG CYS F 452 " distance=2.03 Simple disulfide: pdb=" SG CYS F 487 " - pdb=" SG CYS F 521 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 567 " distance=2.03 Simple disulfide: pdb=" SG CYS F 516 " - pdb=" SG CYS F 577 " distance=2.03 Simple disulfide: pdb=" SG CYS F 547 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS F 592 " - pdb=" SG CYS F 626 " distance=2.03 Simple disulfide: pdb=" SG CYS F 608 " - pdb=" SG CYS F 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 621 " - pdb=" SG CYS F 682 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 662 " distance=2.03 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS F 835 " - pdb=" SG CYS F 869 " distance=2.03 Simple disulfide: pdb=" SG CYS F 864 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F 895 " - pdb=" SG CYS F 905 " distance=2.03 Simple disulfide: pdb=" SG CYS F 938 " - pdb=" SG CYS F 972 " distance=2.03 Simple disulfide: pdb=" SG CYS F 954 " - pdb=" SG CYS F1018 " distance=2.03 Simple disulfide: pdb=" SG CYS F 967 " - pdb=" SG CYS F1028 " distance=2.03 Simple disulfide: pdb=" SG CYS F 998 " - pdb=" SG CYS F1008 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.01 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 728 " - pdb=" SG CYS D 762 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 808 " distance=2.02 Simple disulfide: pdb=" SG CYS D 757 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.03 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG A 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG D1102 " - " ASN D 767 " " NAG D1103 " - " ASN D1027 " " NAG E1101 " - " ASN E 767 " " NAG E1102 " - " ASN E1027 " " NAG F1101 " - " ASN F 445 " " NAG F1102 " - " ASN F 767 " " NAG F1103 " - " ASN F1027 " " NAG X 1 " - " ASN F 320 " " NAG Y 1 " - " ASN D 320 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 815.6 milliseconds 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5268 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 55 sheets defined 24.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 157 through 162 removed outlier: 4.009A pdb=" N THR 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 333 through 346 removed outlier: 4.517A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 346 " --> pdb=" O LYS 2 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.542A pdb=" N GLU E 359 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 360 " --> pdb=" O HIS E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 360' Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 474 through 476 No H-bonds generated for 'chain 'E' and resid 474 through 476' Processing helix chain 'E' and resid 503 through 507 removed outlier: 4.057A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'E' and resid 809 through 813 removed outlier: 3.675A pdb=" N GLU E 812 " --> pdb=" O ARG E 809 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 813 " --> pdb=" O HIS E 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 809 through 813' Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 901 through 905 Processing helix chain 'E' and resid 959 through 971 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1019 through 1023 removed outlier: 3.732A pdb=" N ASP E1023 " --> pdb=" O HIS E1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.805A pdb=" N ASP F 253 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.717A pdb=" N GLN F 344 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS F 345 " --> pdb=" O ILE F 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 341 through 345' Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 403 through 415 removed outlier: 3.557A pdb=" N VAL F 409 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.863A pdb=" N PHE F 507 " --> pdb=" O ASP F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 568 through 572 removed outlier: 3.539A pdb=" N ASP F 572 " --> pdb=" O HIS F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.691A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 867 Processing helix chain 'F' and resid 901 through 905 removed outlier: 3.715A pdb=" N GLN F 904 " --> pdb=" O THR F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 920 removed outlier: 3.560A pdb=" N GLU F 920 " --> pdb=" O PRO F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 971 removed outlier: 3.511A pdb=" N ALA F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1023 removed outlier: 3.565A pdb=" N GLU F1022 " --> pdb=" O GLY F1019 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP F1023 " --> pdb=" O HIS F1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1019 through 1023' Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.542A pdb=" N CYS D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.508A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.057A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.586A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 removed outlier: 3.707A pdb=" N VAL D 755 " --> pdb=" O SER D 751 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 760 " --> pdb=" O VAL D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.592A pdb=" N CYS D 798 " --> pdb=" O ILE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 813 Processing helix chain 'D' and resid 856 through 868 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.778A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.599A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.609A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.693A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'G' and resid 4 through 17 removed outlier: 4.014A pdb=" N LYS G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.217A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 46 removed outlier: 3.813A pdb=" N GLU G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER G 44 " --> pdb=" O PHE G 41 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY G 46 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 57 through 77 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.834A pdb=" N THR G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR G 87 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 119 removed outlier: 3.954A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.158A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.705A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 364 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS E 327 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 371 through 377 removed outlier: 7.027A pdb=" N THR E 471 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 396 through 397 removed outlier: 6.958A pdb=" N LYS E 396 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU E 439 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 477 through 481 removed outlier: 4.033A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB1, first strand: chain 'E' and resid 544 through 545 Processing sheet with id=AB2, first strand: chain 'E' and resid 583 through 586 Processing sheet with id=AB3, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.918A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 649 through 650 Processing sheet with id=AB5, first strand: chain 'E' and resid 719 through 722 Processing sheet with id=AB6, first strand: chain 'E' and resid 719 through 722 removed outlier: 6.047A pdb=" N GLY E 815 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA E 768 " --> pdb=" O GLY E 815 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 817 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 823 through 827 removed outlier: 3.935A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 874 " --> pdb=" O THR E 924 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 823 through 827 removed outlier: 6.437A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP E 889 " --> pdb=" O TRP E 847 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR E 849 " --> pdb=" O TRP E 889 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 930 through 932 removed outlier: 6.849A pdb=" N ASN E1027 " --> pdb=" O LEU E 976 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 930 through 932 removed outlier: 5.975A pdb=" N VAL E 942 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 953 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP E 992 " --> pdb=" O TRP E 950 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 952 " --> pdb=" O TRP E 992 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 279 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 290 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N TRP F 287 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LEU F 330 " --> pdb=" O TRP F 287 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 289 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.858A pdb=" N THR F 471 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.000A pdb=" N VAL F 386 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU F 437 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS F 396 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU F 439 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 477 through 481 Processing sheet with id=AC9, first strand: chain 'F' and resid 477 through 481 removed outlier: 6.324A pdb=" N VAL F 491 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 502 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 498 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP F 541 " --> pdb=" O TRP F 499 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER F 501 " --> pdb=" O TRP F 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 543 through 545 Processing sheet with id=AD2, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.826A pdb=" N ILE F 681 " --> pdb=" O LEU F 630 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.207A pdb=" N VAL F 596 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 607 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP F 646 " --> pdb=" O TRP F 604 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER F 606 " --> pdb=" O TRP F 646 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 649 through 650 Processing sheet with id=AD5, first strand: chain 'F' and resid 719 through 722 removed outlier: 6.012A pdb=" N GLY F 815 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA F 768 " --> pdb=" O GLY F 815 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 817 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 719 through 722 removed outlier: 14.862A pdb=" N GLY F 730 " --> pdb=" O ASP F 745 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N ASP F 745 " --> pdb=" O GLY F 730 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL F 732 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 743 " --> pdb=" O VAL F 732 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 781 " --> pdb=" O TRP F 740 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR F 742 " --> pdb=" O ILE F 781 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F 783 " --> pdb=" O THR F 742 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU F 785 " --> pdb=" O CYS F 744 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP F 746 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 823 through 827 removed outlier: 3.694A pdb=" N TRP F 922 " --> pdb=" O ASN F 876 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 823 through 827 removed outlier: 6.566A pdb=" N LEU F 839 " --> pdb=" O VAL F 850 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 850 " --> pdb=" O LEU F 839 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP F 889 " --> pdb=" O TRP F 847 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR F 849 " --> pdb=" O TRP F 889 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 929 through 932 removed outlier: 6.204A pdb=" N VAL F 942 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 953 " --> pdb=" O VAL F 942 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N TRP F 950 " --> pdb=" O ILE F 991 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N LEU F 993 " --> pdb=" O TRP F 950 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR F 952 " --> pdb=" O LEU F 993 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 929 through 932 Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE3, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS D 327 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 471 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU D 439 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 440 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN D 454 " --> pdb=" O SER D 440 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 476 through 481 Processing sheet with id=AE9, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.398A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 500 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AF2, first strand: chain 'D' and resid 583 through 586 removed outlier: 7.228A pdb=" N ILE D 681 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 583 through 586 removed outlier: 5.280A pdb=" N VAL D 596 " --> pdb=" O LEU D 607 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP D 646 " --> pdb=" O TRP D 604 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER D 606 " --> pdb=" O TRP D 646 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AF5, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF6, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF7, first strand: chain 'D' and resid 823 through 827 removed outlier: 4.158A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 874 " --> pdb=" O THR D 924 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 823 through 827 removed outlier: 6.227A pdb=" N LEU D 839 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.220A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 929 through 932 872 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 9284 1.38 - 1.55: 13928 1.55 - 1.72: 1 1.72 - 1.89: 247 1.89 - 2.06: 8 Bond restraints: 23468 Sorted by residual: bond pdb=" CA SER D 473 " pdb=" CB SER D 473 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" CA SER E 473 " pdb=" CB SER E 473 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.57e-02 4.06e+03 7.57e+00 bond pdb=" N ASP D 745 " pdb=" CA ASP D 745 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" N THR E 471 " pdb=" CA THR E 471 " ideal model delta sigma weight residual 1.464 1.493 -0.030 1.25e-02 6.40e+03 5.64e+00 bond pdb=" CA ALA E 474 " pdb=" CB ALA E 474 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.69e-02 3.50e+03 5.21e+00 ... (remaining 23463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 31437 1.98 - 3.95: 359 3.95 - 5.93: 29 5.93 - 7.90: 1 7.90 - 9.88: 2 Bond angle restraints: 31828 Sorted by residual: angle pdb=" N HIS D 475 " pdb=" CA HIS D 475 " pdb=" C HIS D 475 " ideal model delta sigma weight residual 110.97 101.63 9.34 1.09e+00 8.42e-01 7.34e+01 angle pdb=" N ALA D 474 " pdb=" CA ALA D 474 " pdb=" C ALA D 474 " ideal model delta sigma weight residual 113.50 103.62 9.88 1.65e+00 3.67e-01 3.58e+01 angle pdb=" C HIS D 475 " pdb=" CA HIS D 475 " pdb=" CB HIS D 475 " ideal model delta sigma weight residual 110.96 116.89 -5.93 1.54e+00 4.22e-01 1.48e+01 angle pdb=" CA SER E 473 " pdb=" C SER E 473 " pdb=" O SER E 473 " ideal model delta sigma weight residual 120.90 117.29 3.61 1.03e+00 9.43e-01 1.23e+01 angle pdb=" CA CYS E 472 " pdb=" C CYS E 472 " pdb=" O CYS E 472 " ideal model delta sigma weight residual 121.88 118.12 3.76 1.13e+00 7.83e-01 1.11e+01 ... (remaining 31823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12659 17.88 - 35.76: 1127 35.76 - 53.65: 216 53.65 - 71.53: 45 71.53 - 89.41: 22 Dihedral angle restraints: 14069 sinusoidal: 5804 harmonic: 8265 Sorted by residual: dihedral pdb=" CB CYS F 275 " pdb=" SG CYS F 275 " pdb=" SG CYS F 309 " pdb=" CB CYS F 309 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 355 " pdb=" CB CYS E 355 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 14066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2694 0.050 - 0.099: 595 0.099 - 0.149: 114 0.149 - 0.198: 3 0.198 - 0.248: 1 Chirality restraints: 3407 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" CA PHE F 283 " pdb=" N PHE F 283 " pdb=" C PHE F 283 " pdb=" CB PHE F 283 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO F 591 " pdb=" N PRO F 591 " pdb=" C PRO F 591 " pdb=" CB PRO F 591 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 3404 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 903 " 0.013 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP D 903 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 903 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 903 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 903 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 903 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 903 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 903 " 0.012 2.00e-02 2.50e+03 1.73e-02 7.50e+00 pdb=" CG TRP F 903 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP F 903 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 903 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 903 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 903 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 903 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 281 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL F 281 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL F 281 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG F 282 " 0.013 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 313 2.60 - 3.18: 19227 3.18 - 3.75: 37612 3.75 - 4.33: 52720 4.33 - 4.90: 86501 Nonbonded interactions: 196373 Sorted by model distance: nonbonded pdb=" OE2 GLU D 812 " pdb="CA CA D1107 " model vdw 2.025 3.250 nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP E 784 " pdb="CA CA E1105 " model vdw 2.163 3.250 nonbonded pdb=" O MET F 786 " pdb="CA CA F1107 " model vdw 2.168 3.250 nonbonded pdb=" OD1 ASP F 749 " pdb="CA CA F1107 " model vdw 2.182 3.250 ... (remaining 196368 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' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'D' and (resid 154 through 828 or resid 835 through 1112)) selection = (chain 'F' and (resid 154 through 691 or resid 718 through 1112)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 19.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 23579 Z= 0.151 Angle : 0.527 9.879 32062 Z= 0.296 Chirality : 0.042 0.248 3407 Planarity : 0.003 0.053 4125 Dihedral : 13.857 89.408 8522 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 0.16 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2934 helix: 1.68 (0.23), residues: 532 sheet: -0.83 (0.26), residues: 401 loop : -0.82 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 381 TYR 0.013 0.001 TYR 2 221 PHE 0.009 0.001 PHE 2 280 TRP 0.046 0.001 TRP D 903 HIS 0.007 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (23468) covalent geometry : angle 0.52185 / 0.30 (31828) SS BOND : bond 0.00324 / 0.15 ( 93) SS BOND : angle 0.93970 / 0.58 ( 186) hydrogen bonds : bond 0.21931 / 14.28 ( 765) hydrogen bonds : angle 8.32673 / 5.78 ( 2352) Misc. bond : bond 0.09347 / 4.51 ( 2) link_BETA1-4 : bond 0.00352 / 0.18 ( 3) link_BETA1-4 : angle 1.25924 / 0.61 ( 9) link_NAG-ASN : bond 0.00237 / 0.12 ( 13) link_NAG-ASN : angle 1.15704 / 0.67 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 494 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 156 LYS cc_start: 0.8160 (tttt) cc_final: 0.7828 (tttp) REVERT: 2 184 SER cc_start: 0.8877 (m) cc_final: 0.8516 (p) REVERT: 2 202 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.6935 (mmm160) REVERT: 2 248 ASP cc_start: 0.8031 (m-30) cc_final: 0.7800 (m-30) REVERT: 2 306 GLU cc_start: 0.7361 (mp0) cc_final: 0.6976 (mp0) REVERT: 2 308 ASP cc_start: 0.8519 (t0) cc_final: 0.8150 (t0) REVERT: 2 341 GLN cc_start: 0.7587 (mm110) cc_final: 0.7326 (mt0) REVERT: E 299 ASP cc_start: 0.6206 (m-30) cc_final: 0.5979 (m-30) REVERT: E 442 CYS cc_start: 0.4242 (t) cc_final: 0.3762 (t) REVERT: E 532 HIS cc_start: 0.8508 (t-90) cc_final: 0.8251 (t70) REVERT: E 544 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7240 (tt0) REVERT: E 550 HIS cc_start: 0.7559 (p90) cc_final: 0.7237 (p90) REVERT: E 615 GLU cc_start: 0.7551 (mp0) cc_final: 0.7275 (mp0) REVERT: E 764 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7636 (pt0) REVERT: E 938 CYS cc_start: 0.6522 (m) cc_final: 0.6163 (m) REVERT: E 995 GLU cc_start: 0.7228 (tt0) cc_final: 0.6738 (tm-30) REVERT: E 997 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6229 (mmtt) REVERT: E 999 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7388 (mmtt) REVERT: F 167 MET cc_start: 0.5833 (mmp) cc_final: 0.5542 (ttp) REVERT: F 187 ASN cc_start: 0.8639 (t0) cc_final: 0.7811 (t0) REVERT: F 240 HIS cc_start: 0.6341 (p90) cc_final: 0.5484 (p90) REVERT: F 253 ASP cc_start: 0.7111 (m-30) cc_final: 0.6879 (m-30) REVERT: F 446 GLU cc_start: 0.7728 (mp0) cc_final: 0.7335 (mp0) REVERT: F 612 TRP cc_start: 0.7678 (t-100) cc_final: 0.7413 (t-100) REVERT: F 649 MET cc_start: 0.8157 (mtm) cc_final: 0.7827 (mtt) REVERT: F 723 ASN cc_start: 0.7812 (t0) cc_final: 0.7576 (m-40) REVERT: F 859 THR cc_start: 0.7949 (m) cc_final: 0.7691 (p) REVERT: F 922 TRP cc_start: 0.8159 (m100) cc_final: 0.7941 (m100) REVERT: F 1011 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7621 (ttp-170) REVERT: D 245 LYS cc_start: 0.8015 (mptt) cc_final: 0.7814 (tttp) REVERT: D 456 GLN cc_start: 0.8897 (mt0) cc_final: 0.8695 (mt0) REVERT: D 550 HIS cc_start: 0.7838 (p-80) cc_final: 0.7583 (p-80) REVERT: D 825 ARG cc_start: 0.8365 (ptt180) cc_final: 0.8013 (ptt-90) REVERT: D 1004 SER cc_start: 0.8528 (p) cc_final: 0.8267 (t) REVERT: G 9 SER cc_start: 0.8764 (p) cc_final: 0.8486 (p) REVERT: G 132 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8668 (mtpp) outliers start: 3 outliers final: 1 residues processed: 496 average time/residue: 0.1708 time to fit residues: 129.0583 Evaluate side-chains 250 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 473 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 475 HIS E 550 HIS E 723 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 HIS F 284 GLN F 306 GLN F 464 HIS F 587 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 HIS D 964 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139508 restraints weight = 29171.455| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.29 r_work: 0.3392 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 23579 Z= 0.177 Angle : 0.587 10.126 32062 Z= 0.307 Chirality : 0.046 0.590 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.973 79.086 3476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 1.56 % Allowed : 8.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2934 helix: 1.87 (0.23), residues: 532 sheet: -0.94 (0.25), residues: 410 loop : -0.86 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 412 TYR 0.018 0.001 TYR 2 183 PHE 0.015 0.001 PHE 2 300 TRP 0.017 0.001 TRP D 922 HIS 0.008 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (23468) covalent geometry : angle 0.57750 / 0.30 (31828) SS BOND : bond 0.00409 / 0.23 ( 93) SS BOND : angle 1.23274 / 0.82 ( 186) hydrogen bonds : bond 0.04280 / 2.71 ( 765) hydrogen bonds : angle 5.59468 / 3.86 ( 2352) Misc. bond : bond 0.10800 / 5.18 ( 2) link_BETA1-4 : bond 0.00388 / 0.20 ( 3) link_BETA1-4 : angle 1.30823 / 0.60 ( 9) link_NAG-ASN : bond 0.00587 / 0.41 ( 13) link_NAG-ASN : angle 1.94504 / 1.44 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.7842 (mmm160) REVERT: 2 308 ASP cc_start: 0.8607 (t0) cc_final: 0.8330 (t0) REVERT: 2 337 GLN cc_start: 0.8354 (tt0) cc_final: 0.8013 (mt0) REVERT: E 299 ASP cc_start: 0.6029 (m-30) cc_final: 0.5660 (m-30) REVERT: E 406 GLU cc_start: 0.7535 (mp0) cc_final: 0.7275 (mp0) REVERT: E 466 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5877 (pm20) REVERT: E 532 HIS cc_start: 0.8623 (t-90) cc_final: 0.8371 (t70) REVERT: E 544 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7016 (tt0) REVERT: E 615 GLU cc_start: 0.7872 (mp0) cc_final: 0.7497 (mp0) REVERT: E 671 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (mm) REVERT: E 764 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7742 (pt0) REVERT: E 820 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7999 (mt-10) REVERT: E 891 ASP cc_start: 0.8575 (t0) cc_final: 0.8310 (t0) REVERT: E 938 CYS cc_start: 0.6769 (m) cc_final: 0.6397 (m) REVERT: E 970 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7358 (mp) REVERT: E 995 GLU cc_start: 0.7387 (tt0) cc_final: 0.6661 (tm-30) REVERT: E 996 VAL cc_start: 0.7252 (m) cc_final: 0.6857 (p) REVERT: E 997 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6190 (mmtt) REVERT: F 167 MET cc_start: 0.6194 (mmp) cc_final: 0.5655 (ttp) REVERT: F 187 ASN cc_start: 0.8779 (t0) cc_final: 0.8145 (t0) REVERT: F 240 HIS cc_start: 0.6500 (p90) cc_final: 0.5773 (p90) REVERT: F 346 LYS cc_start: 0.7498 (mmtm) cc_final: 0.7026 (ptmm) REVERT: F 352 LYS cc_start: 0.7578 (tttm) cc_final: 0.7035 (tmtt) REVERT: F 446 GLU cc_start: 0.7942 (mp0) cc_final: 0.7670 (mp0) REVERT: F 541 TRP cc_start: 0.8681 (m100) cc_final: 0.8366 (m100) REVERT: F 649 MET cc_start: 0.8334 (mtm) cc_final: 0.8084 (mtt) REVERT: F 723 ASN cc_start: 0.8034 (t0) cc_final: 0.7796 (m-40) REVERT: F 914 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7892 (mp) REVERT: F 922 TRP cc_start: 0.8291 (m100) cc_final: 0.7731 (m100) REVERT: F 1011 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7823 (ttp-170) REVERT: D 622 GLN cc_start: 0.8600 (tp40) cc_final: 0.8357 (tp40) REVERT: D 740 TRP cc_start: 0.8273 (m100) cc_final: 0.8026 (m100) REVERT: D 825 ARG cc_start: 0.8643 (ptt180) cc_final: 0.8107 (ptt-90) REVERT: D 922 TRP cc_start: 0.8344 (m100) cc_final: 0.8083 (m100) outliers start: 38 outliers final: 20 residues processed: 306 average time/residue: 0.1547 time to fit residues: 74.1263 Evaluate side-chains 253 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 964 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 82 optimal weight: 0.0770 chunk 273 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 264 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 456 GLN E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139799 restraints weight = 29012.147| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.21 r_work: 0.3335 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 23579 Z= 0.195 Angle : 0.570 9.170 32062 Z= 0.298 Chirality : 0.044 0.166 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.827 80.518 3475 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 11.63 % Favored : 86.23 % 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: -0.64 (0.15), residues: 2934 helix: 1.78 (0.23), residues: 529 sheet: -1.19 (0.25), residues: 368 loop : -0.92 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 376 TYR 0.023 0.002 TYR 2 183 PHE 0.014 0.001 PHE 2 300 TRP 0.014 0.001 TRP F 796 HIS 0.010 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (23468) covalent geometry : angle 0.56117 / 0.30 (31828) SS BOND : bond 0.00374 / 0.23 ( 93) SS BOND : angle 1.08904 / 0.72 ( 186) hydrogen bonds : bond 0.03810 / 2.41 ( 765) hydrogen bonds : angle 5.17636 / 3.58 ( 2352) Misc. bond : bond 0.12631 / 6.06 ( 2) link_BETA1-4 : bond 0.00297 / 0.11 ( 3) link_BETA1-4 : angle 1.48903 / 0.71 ( 9) link_NAG-ASN : bond 0.00340 / 0.23 ( 13) link_NAG-ASN : angle 1.97961 / 1.34 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.7908 (mmm160) REVERT: 2 308 ASP cc_start: 0.8718 (t0) cc_final: 0.8404 (t0) REVERT: 2 337 GLN cc_start: 0.8531 (tt0) cc_final: 0.8062 (tt0) REVERT: E 299 ASP cc_start: 0.6148 (m-30) cc_final: 0.5737 (m-30) REVERT: E 406 GLU cc_start: 0.7466 (mp0) cc_final: 0.7035 (mm-30) REVERT: E 466 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6010 (pm20) REVERT: E 532 HIS cc_start: 0.8675 (t-90) cc_final: 0.8442 (t70) REVERT: E 544 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7058 (tt0) REVERT: E 615 GLU cc_start: 0.7993 (mp0) cc_final: 0.7579 (mp0) REVERT: E 671 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8206 (mm) REVERT: E 764 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7832 (pt0) REVERT: E 820 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8217 (mt-10) REVERT: E 938 CYS cc_start: 0.6756 (m) cc_final: 0.6472 (m) REVERT: E 970 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7486 (mp) REVERT: E 995 GLU cc_start: 0.7481 (tt0) cc_final: 0.7097 (tm-30) REVERT: E 997 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6767 (mmmt) REVERT: F 167 MET cc_start: 0.6321 (mmp) cc_final: 0.5810 (ttp) REVERT: F 187 ASN cc_start: 0.8693 (t0) cc_final: 0.8025 (t0) REVERT: F 240 HIS cc_start: 0.6664 (p90) cc_final: 0.5870 (p90) REVERT: F 649 MET cc_start: 0.8405 (mtm) cc_final: 0.8173 (mtt) REVERT: F 723 ASN cc_start: 0.8110 (t0) cc_final: 0.7867 (m-40) REVERT: F 801 HIS cc_start: 0.6924 (m-70) cc_final: 0.6653 (m90) REVERT: F 835 CYS cc_start: 0.6538 (m) cc_final: 0.6302 (m) REVERT: F 914 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7935 (mp) REVERT: F 922 TRP cc_start: 0.8139 (m100) cc_final: 0.7619 (m-10) REVERT: F 938 CYS cc_start: 0.6766 (m) cc_final: 0.6526 (m) REVERT: D 550 HIS cc_start: 0.8206 (p-80) cc_final: 0.7844 (p90) REVERT: D 825 ARG cc_start: 0.8711 (ptt180) cc_final: 0.8092 (ptt-90) REVERT: D 922 TRP cc_start: 0.8524 (m100) cc_final: 0.8228 (m100) REVERT: D 964 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: D 1004 SER cc_start: 0.8892 (t) cc_final: 0.8082 (p) REVERT: C 56 LYS cc_start: 0.8194 (tttt) cc_final: 0.7608 (mmtt) REVERT: C 126 ASP cc_start: 0.8989 (t70) cc_final: 0.8771 (t0) REVERT: G 14 LEU cc_start: 0.8808 (tp) cc_final: 0.8490 (tp) outliers start: 52 outliers final: 27 residues processed: 290 average time/residue: 0.1483 time to fit residues: 68.3903 Evaluate side-chains 252 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 281 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 187 ASN D 475 HIS D 964 GLN G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.179081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140282 restraints weight = 28783.258| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.24 r_work: 0.3342 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 23579 Z= 0.147 Angle : 0.528 8.942 32062 Z= 0.278 Chirality : 0.043 0.357 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.570 79.833 3475 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 2.18 % Allowed : 13.11 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 2934 helix: 1.99 (0.23), residues: 529 sheet: -1.21 (0.26), residues: 340 loop : -0.90 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 376 TYR 0.019 0.001 TYR 2 183 PHE 0.012 0.001 PHE 2 300 TRP 0.014 0.001 TRP D 922 HIS 0.007 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (23468) covalent geometry : angle 0.51979 / 0.28 (31828) SS BOND : bond 0.00347 / 0.20 ( 93) SS BOND : angle 0.94333 / 0.65 ( 186) hydrogen bonds : bond 0.03377 / 2.13 ( 765) hydrogen bonds : angle 4.90535 / 3.38 ( 2352) Misc. bond : bond 0.10491 / 5.06 ( 2) link_BETA1-4 : bond 0.00301 / 0.15 ( 3) link_BETA1-4 : angle 1.37166 / 0.66 ( 9) link_NAG-ASN : bond 0.00291 / 0.20 ( 13) link_NAG-ASN : angle 1.90752 / 1.24 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7898 (mmm160) REVERT: 2 308 ASP cc_start: 0.8688 (t0) cc_final: 0.8353 (t0) REVERT: E 299 ASP cc_start: 0.6136 (m-30) cc_final: 0.5734 (m-30) REVERT: E 406 GLU cc_start: 0.7417 (mp0) cc_final: 0.7011 (mm-30) REVERT: E 466 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: E 532 HIS cc_start: 0.8596 (t-90) cc_final: 0.8350 (t70) REVERT: E 544 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7039 (tt0) REVERT: E 615 GLU cc_start: 0.7991 (mp0) cc_final: 0.7562 (mp0) REVERT: E 671 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8248 (mm) REVERT: E 764 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7808 (pt0) REVERT: E 820 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8201 (mt-10) REVERT: E 938 CYS cc_start: 0.6693 (m) cc_final: 0.6487 (m) REVERT: E 970 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 995 GLU cc_start: 0.7454 (tt0) cc_final: 0.7177 (tm-30) REVERT: E 996 VAL cc_start: 0.7413 (m) cc_final: 0.7025 (p) REVERT: E 997 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6608 (mmmt) REVERT: F 167 MET cc_start: 0.6324 (mmp) cc_final: 0.5845 (ttp) REVERT: F 187 ASN cc_start: 0.8626 (t0) cc_final: 0.8028 (t0) REVERT: F 240 HIS cc_start: 0.6584 (p90) cc_final: 0.5870 (p90) REVERT: F 723 ASN cc_start: 0.8064 (t0) cc_final: 0.7834 (m-40) REVERT: F 801 HIS cc_start: 0.6968 (m-70) cc_final: 0.6734 (m90) REVERT: F 835 CYS cc_start: 0.6636 (m) cc_final: 0.6402 (m) REVERT: F 922 TRP cc_start: 0.8103 (m100) cc_final: 0.7627 (m-10) REVERT: F 938 CYS cc_start: 0.7014 (m) cc_final: 0.6748 (m) REVERT: D 344 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: D 742 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.6939 (m) REVERT: D 825 ARG cc_start: 0.8634 (ptt180) cc_final: 0.8031 (ptt-90) REVERT: D 922 TRP cc_start: 0.8563 (m100) cc_final: 0.8251 (m100) REVERT: D 1004 SER cc_start: 0.8860 (t) cc_final: 0.8045 (p) REVERT: C 56 LYS cc_start: 0.8130 (tttt) cc_final: 0.7583 (mmtt) REVERT: C 126 ASP cc_start: 0.9002 (t70) cc_final: 0.8798 (t0) REVERT: G 14 LEU cc_start: 0.8816 (tp) cc_final: 0.8538 (tp) outliers start: 53 outliers final: 30 residues processed: 284 average time/residue: 0.1514 time to fit residues: 67.9123 Evaluate side-chains 251 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 257 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 327 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 187 ASN D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137725 restraints weight = 28811.327| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.10 r_work: 0.3321 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 23579 Z= 0.210 Angle : 0.564 9.189 32062 Z= 0.294 Chirality : 0.045 0.236 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.574 80.016 3475 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 13.36 % Favored : 83.68 % 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: -0.67 (0.15), residues: 2934 helix: 1.80 (0.22), residues: 529 sheet: -1.29 (0.25), residues: 363 loop : -0.94 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 376 TYR 0.017 0.002 TYR 2 183 PHE 0.015 0.001 PHE 2 280 TRP 0.014 0.001 TRP F 796 HIS 0.008 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (23468) covalent geometry : angle 0.55435 / 0.29 (31828) SS BOND : bond 0.00402 / 0.26 ( 93) SS BOND : angle 1.21660 / 0.81 ( 186) hydrogen bonds : bond 0.03476 / 2.20 ( 765) hydrogen bonds : angle 4.93152 / 3.39 ( 2352) Misc. bond : bond 0.13046 / 6.26 ( 2) link_BETA1-4 : bond 0.00131 / 0.05 ( 3) link_BETA1-4 : angle 1.58767 / 0.77 ( 9) link_NAG-ASN : bond 0.00212 / 0.12 ( 13) link_NAG-ASN : angle 1.86337 / 1.22 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.7889 (mmm160) REVERT: 2 308 ASP cc_start: 0.8748 (t0) cc_final: 0.8453 (t0) REVERT: E 299 ASP cc_start: 0.6145 (m-30) cc_final: 0.5725 (m-30) REVERT: E 358 ASN cc_start: 0.7014 (m-40) cc_final: 0.6787 (m-40) REVERT: E 392 ARG cc_start: 0.7542 (mpt-90) cc_final: 0.7184 (mtm110) REVERT: E 406 GLU cc_start: 0.7437 (mp0) cc_final: 0.7034 (mm-30) REVERT: E 532 HIS cc_start: 0.8658 (t-90) cc_final: 0.8398 (t70) REVERT: E 544 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7066 (tt0) REVERT: E 671 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8341 (mm) REVERT: E 764 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7947 (pt0) REVERT: E 820 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8313 (mt-10) REVERT: E 995 GLU cc_start: 0.7605 (tt0) cc_final: 0.7234 (tm-30) REVERT: E 996 VAL cc_start: 0.7398 (m) cc_final: 0.7074 (p) REVERT: E 997 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6610 (mmmt) REVERT: F 167 MET cc_start: 0.6428 (mmp) cc_final: 0.5888 (ttp) REVERT: F 187 ASN cc_start: 0.8644 (t0) cc_final: 0.8022 (t0) REVERT: F 240 HIS cc_start: 0.6782 (p90) cc_final: 0.5988 (p90) REVERT: F 241 GLN cc_start: 0.7467 (pp30) cc_final: 0.7151 (pp30) REVERT: F 723 ASN cc_start: 0.8128 (t0) cc_final: 0.7884 (m-40) REVERT: F 785 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7825 (mm-30) REVERT: F 801 HIS cc_start: 0.7075 (m-70) cc_final: 0.6869 (m90) REVERT: F 903 TRP cc_start: 0.8277 (m-10) cc_final: 0.7760 (m100) REVERT: F 922 TRP cc_start: 0.8173 (m100) cc_final: 0.7806 (m100) REVERT: D 344 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: D 550 HIS cc_start: 0.8241 (p-80) cc_final: 0.7902 (p90) REVERT: D 742 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7142 (m) REVERT: D 825 ARG cc_start: 0.8681 (ptt180) cc_final: 0.8055 (ptt-90) REVERT: D 922 TRP cc_start: 0.8611 (m100) cc_final: 0.8252 (m100) REVERT: D 1004 SER cc_start: 0.8806 (t) cc_final: 0.7992 (p) REVERT: C 56 LYS cc_start: 0.8196 (tttt) cc_final: 0.7613 (mmtt) REVERT: C 126 ASP cc_start: 0.9013 (t70) cc_final: 0.8783 (t0) REVERT: G 14 LEU cc_start: 0.8802 (tp) cc_final: 0.8552 (tp) outliers start: 72 outliers final: 53 residues processed: 286 average time/residue: 0.1566 time to fit residues: 71.0509 Evaluate side-chains 268 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 242 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 132 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 187 ASN D 240 HIS D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 GLN G 2 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140536 restraints weight = 28870.779| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.12 r_work: 0.3366 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 23579 Z= 0.117 Angle : 0.511 9.404 32062 Z= 0.268 Chirality : 0.042 0.196 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.306 78.034 3475 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 2.47 % Allowed : 14.80 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2934 helix: 2.05 (0.23), residues: 531 sheet: -1.23 (0.26), residues: 330 loop : -0.86 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 376 TYR 0.016 0.001 TYR 2 183 PHE 0.011 0.001 PHE 2 300 TRP 0.012 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (23468) covalent geometry : angle 0.50394 / 0.27 (31828) SS BOND : bond 0.00239 / 0.15 ( 93) SS BOND : angle 0.98483 / 0.65 ( 186) hydrogen bonds : bond 0.03105 / 1.96 ( 765) hydrogen bonds : angle 4.67576 / 3.21 ( 2352) Misc. bond : bond 0.08617 / 4.18 ( 2) link_BETA1-4 : bond 0.00304 / 0.14 ( 3) link_BETA1-4 : angle 1.31757 / 0.63 ( 9) link_NAG-ASN : bond 0.00187 / 0.11 ( 13) link_NAG-ASN : angle 1.62835 / 1.03 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.7886 (mmm160) REVERT: 2 308 ASP cc_start: 0.8702 (t0) cc_final: 0.8368 (t0) REVERT: E 299 ASP cc_start: 0.6121 (m-30) cc_final: 0.5715 (m-30) REVERT: E 376 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7520 (ttp-110) REVERT: E 392 ARG cc_start: 0.7524 (mpt-90) cc_final: 0.7182 (mtm110) REVERT: E 406 GLU cc_start: 0.7411 (mp0) cc_final: 0.7002 (mm-30) REVERT: E 466 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6148 (pm20) REVERT: E 532 HIS cc_start: 0.8590 (t-90) cc_final: 0.8347 (t70) REVERT: E 544 GLU cc_start: 0.7722 (tm-30) cc_final: 0.6992 (tt0) REVERT: E 671 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8286 (mm) REVERT: E 764 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7863 (pt0) REVERT: E 820 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8319 (mt-10) REVERT: E 855 MET cc_start: 0.7296 (ttm) cc_final: 0.7068 (ttm) REVERT: E 995 GLU cc_start: 0.7633 (tt0) cc_final: 0.7304 (tm-30) REVERT: E 997 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6647 (mmmt) REVERT: F 167 MET cc_start: 0.6356 (mmp) cc_final: 0.5848 (ttp) REVERT: F 240 HIS cc_start: 0.6673 (p90) cc_final: 0.5965 (p90) REVERT: F 645 ILE cc_start: 0.7926 (mm) cc_final: 0.7540 (pt) REVERT: F 723 ASN cc_start: 0.8054 (t0) cc_final: 0.7807 (m-40) REVERT: F 785 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7752 (mm-30) REVERT: F 801 HIS cc_start: 0.7083 (m-70) cc_final: 0.6864 (m90) REVERT: F 922 TRP cc_start: 0.8102 (m100) cc_final: 0.7772 (m100) REVERT: F 938 CYS cc_start: 0.6955 (m) cc_final: 0.6689 (m) REVERT: D 187 ASN cc_start: 0.7971 (m-40) cc_final: 0.7745 (m110) REVERT: D 344 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: D 539 GLN cc_start: 0.7834 (pm20) cc_final: 0.7523 (tt0) REVERT: D 550 HIS cc_start: 0.8208 (p-80) cc_final: 0.7911 (p90) REVERT: D 742 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7097 (m) REVERT: D 749 ASP cc_start: 0.6641 (t0) cc_final: 0.6367 (t0) REVERT: D 752 ASP cc_start: 0.5653 (m-30) cc_final: 0.5321 (m-30) REVERT: D 825 ARG cc_start: 0.8641 (ptt180) cc_final: 0.8128 (ptt-90) REVERT: D 922 TRP cc_start: 0.8506 (m100) cc_final: 0.8225 (m100) REVERT: D 1004 SER cc_start: 0.8835 (t) cc_final: 0.8051 (p) REVERT: C 56 LYS cc_start: 0.8160 (tttt) cc_final: 0.7601 (mmtt) REVERT: G 14 LEU cc_start: 0.8758 (tp) cc_final: 0.8516 (tp) REVERT: G 90 GLU cc_start: 0.8644 (tp30) cc_final: 0.8345 (tp30) outliers start: 60 outliers final: 43 residues processed: 287 average time/residue: 0.1526 time to fit residues: 69.4927 Evaluate side-chains 264 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 289 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 723 ASN F 648 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136373 restraints weight = 29071.516| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.34 r_work: 0.3262 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.188 23579 Z= 0.233 Angle : 0.580 7.265 32062 Z= 0.303 Chirality : 0.045 0.218 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.500 80.607 3475 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 3.04 % Allowed : 15.00 % Favored : 81.96 % 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: -0.70 (0.15), residues: 2934 helix: 1.72 (0.22), residues: 533 sheet: -1.35 (0.26), residues: 327 loop : -0.94 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 376 TYR 0.020 0.002 TYR D 465 PHE 0.017 0.002 PHE 2 280 TRP 0.016 0.001 TRP F 796 HIS 0.008 0.001 HIS G 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (23468) covalent geometry : angle 0.57047 / 0.30 (31828) SS BOND : bond 0.00444 / 0.28 ( 93) SS BOND : angle 1.23408 / 0.81 ( 186) hydrogen bonds : bond 0.03466 / 2.20 ( 765) hydrogen bonds : angle 4.88946 / 3.36 ( 2352) Misc. bond : bond 0.13722 / 6.58 ( 2) link_BETA1-4 : bond 0.00315 / 0.14 ( 3) link_BETA1-4 : angle 1.65745 / 0.80 ( 9) link_NAG-ASN : bond 0.00244 / 0.13 ( 13) link_NAG-ASN : angle 1.87650 / 1.22 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 232 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7784 (mmm160) REVERT: 2 308 ASP cc_start: 0.8594 (t0) cc_final: 0.8322 (t0) REVERT: E 299 ASP cc_start: 0.6159 (m-30) cc_final: 0.5740 (m-30) REVERT: E 392 ARG cc_start: 0.7445 (mpt-90) cc_final: 0.7233 (mtm110) REVERT: E 406 GLU cc_start: 0.7343 (mp0) cc_final: 0.6960 (mm-30) REVERT: E 466 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: E 532 HIS cc_start: 0.8645 (t-90) cc_final: 0.8382 (t70) REVERT: E 544 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7028 (tt0) REVERT: E 671 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8364 (mm) REVERT: E 764 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7926 (pt0) REVERT: E 855 MET cc_start: 0.7251 (ttm) cc_final: 0.7020 (ttm) REVERT: E 995 GLU cc_start: 0.7594 (tt0) cc_final: 0.7321 (tm-30) REVERT: E 997 LYS cc_start: 0.7008 (mmtt) cc_final: 0.6711 (mmmt) REVERT: F 167 MET cc_start: 0.6332 (mmp) cc_final: 0.5855 (ttp) REVERT: F 187 ASN cc_start: 0.8602 (t0) cc_final: 0.7761 (t0) REVERT: F 226 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6450 (mt) REVERT: F 240 HIS cc_start: 0.6713 (p90) cc_final: 0.6030 (p90) REVERT: F 241 GLN cc_start: 0.7667 (pp30) cc_final: 0.7256 (pp30) REVERT: F 645 ILE cc_start: 0.7982 (mm) cc_final: 0.7618 (pt) REVERT: F 723 ASN cc_start: 0.8035 (t0) cc_final: 0.7803 (m-40) REVERT: F 785 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7408 (mm-30) REVERT: F 801 HIS cc_start: 0.7094 (m-70) cc_final: 0.6845 (m90) REVERT: F 922 TRP cc_start: 0.8123 (m100) cc_final: 0.7878 (m100) REVERT: F 938 CYS cc_start: 0.6612 (m) cc_final: 0.6324 (m) REVERT: D 344 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: D 550 HIS cc_start: 0.8179 (p-80) cc_final: 0.7905 (p90) REVERT: D 580 TYR cc_start: 0.8546 (p90) cc_final: 0.7999 (p90) REVERT: D 742 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7398 (m) REVERT: D 825 ARG cc_start: 0.8535 (ptt180) cc_final: 0.7895 (ptt-90) REVERT: D 1004 SER cc_start: 0.8707 (t) cc_final: 0.7932 (p) REVERT: C 56 LYS cc_start: 0.7974 (tttt) cc_final: 0.7525 (mmtt) REVERT: C 126 ASP cc_start: 0.8739 (t70) cc_final: 0.8477 (t0) REVERT: G 14 LEU cc_start: 0.8767 (tp) cc_final: 0.8534 (tp) outliers start: 74 outliers final: 53 residues processed: 290 average time/residue: 0.1441 time to fit residues: 66.4851 Evaluate side-chains 273 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 207 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140210 restraints weight = 28764.916| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.16 r_work: 0.3330 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 23579 Z= 0.153 Angle : 0.533 11.211 32062 Z= 0.279 Chirality : 0.043 0.242 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.313 79.936 3475 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.79 % Allowed : 15.45 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 2934 helix: 1.90 (0.23), residues: 535 sheet: -1.26 (0.26), residues: 325 loop : -0.92 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 376 TYR 0.026 0.001 TYR D 465 PHE 0.012 0.001 PHE 2 300 TRP 0.015 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (23468) covalent geometry : angle 0.52537 / 0.28 (31828) SS BOND : bond 0.00297 / 0.19 ( 93) SS BOND : angle 1.05060 / 0.69 ( 186) hydrogen bonds : bond 0.03192 / 2.01 ( 765) hydrogen bonds : angle 4.71636 / 3.24 ( 2352) Misc. bond : bond 0.10361 / 5.01 ( 2) link_BETA1-4 : bond 0.00275 / 0.13 ( 3) link_BETA1-4 : angle 1.41827 / 0.68 ( 9) link_NAG-ASN : bond 0.00192 / 0.10 ( 13) link_NAG-ASN : angle 1.69488 / 1.07 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.7905 (mmm160) REVERT: 2 308 ASP cc_start: 0.8792 (t0) cc_final: 0.8524 (t0) REVERT: E 299 ASP cc_start: 0.6160 (m-30) cc_final: 0.5736 (m-30) REVERT: E 376 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7358 (ttp-110) REVERT: E 392 ARG cc_start: 0.7522 (mpt-90) cc_final: 0.7260 (mtm110) REVERT: E 406 GLU cc_start: 0.7409 (mp0) cc_final: 0.6885 (mp0) REVERT: E 466 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: E 532 HIS cc_start: 0.8648 (t-90) cc_final: 0.8401 (t70) REVERT: E 544 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7047 (tt0) REVERT: E 671 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8347 (mm) REVERT: E 764 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7823 (pt0) REVERT: E 995 GLU cc_start: 0.7653 (tt0) cc_final: 0.7322 (tm-30) REVERT: E 996 VAL cc_start: 0.7516 (m) cc_final: 0.7174 (p) REVERT: E 997 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6680 (mmmt) REVERT: F 167 MET cc_start: 0.6489 (mmp) cc_final: 0.5985 (ttp) REVERT: F 187 ASN cc_start: 0.8663 (t0) cc_final: 0.7858 (t0) REVERT: F 226 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6625 (mt) REVERT: F 240 HIS cc_start: 0.6721 (p90) cc_final: 0.6075 (p90) REVERT: F 241 GLN cc_start: 0.7695 (pp30) cc_final: 0.7337 (pp30) REVERT: F 723 ASN cc_start: 0.8078 (t0) cc_final: 0.7839 (m-40) REVERT: F 801 HIS cc_start: 0.7095 (m-70) cc_final: 0.6893 (m90) REVERT: F 922 TRP cc_start: 0.8223 (m100) cc_final: 0.8018 (m100) REVERT: F 938 CYS cc_start: 0.7033 (m) cc_final: 0.6758 (m) REVERT: D 263 ASP cc_start: 0.7407 (t0) cc_final: 0.6713 (p0) REVERT: D 344 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: D 550 HIS cc_start: 0.8261 (p-80) cc_final: 0.7932 (p90) REVERT: D 580 TYR cc_start: 0.8592 (p90) cc_final: 0.8110 (p90) REVERT: D 736 HIS cc_start: 0.4918 (OUTLIER) cc_final: 0.4364 (p-80) REVERT: D 742 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7430 (m) REVERT: D 825 ARG cc_start: 0.8665 (ptt180) cc_final: 0.8085 (ptt-90) REVERT: D 922 TRP cc_start: 0.8471 (m100) cc_final: 0.8140 (m100) REVERT: D 1004 SER cc_start: 0.8790 (t) cc_final: 0.8013 (p) REVERT: C 56 LYS cc_start: 0.8080 (tttt) cc_final: 0.7555 (mmtt) REVERT: C 90 LYS cc_start: 0.8914 (tttp) cc_final: 0.8692 (tttp) outliers start: 68 outliers final: 52 residues processed: 281 average time/residue: 0.1602 time to fit residues: 71.6259 Evaluate side-chains 276 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 124 HIS Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 44 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137622 restraints weight = 28950.409| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.26 r_work: 0.3306 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 23579 Z= 0.167 Angle : 0.540 9.920 32062 Z= 0.282 Chirality : 0.044 0.220 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.284 80.135 3475 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 2.92 % Allowed : 15.58 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2934 helix: 1.91 (0.22), residues: 535 sheet: -1.31 (0.26), residues: 327 loop : -0.91 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.025 0.002 TYR D 465 PHE 0.013 0.001 PHE 2 300 TRP 0.017 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (23468) covalent geometry : angle 0.53165 / 0.28 (31828) SS BOND : bond 0.00330 / 0.21 ( 93) SS BOND : angle 1.06511 / 0.70 ( 186) hydrogen bonds : bond 0.03208 / 2.03 ( 765) hydrogen bonds : angle 4.71073 / 3.24 ( 2352) Misc. bond : bond 0.10920 / 5.27 ( 2) link_BETA1-4 : bond 0.00259 / 0.12 ( 3) link_BETA1-4 : angle 1.43613 / 0.68 ( 9) link_NAG-ASN : bond 0.00196 / 0.10 ( 13) link_NAG-ASN : angle 1.70814 / 1.08 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.7912 (mmm160) REVERT: 2 308 ASP cc_start: 0.8819 (t0) cc_final: 0.8551 (t0) REVERT: E 299 ASP cc_start: 0.6171 (m-30) cc_final: 0.5737 (m-30) REVERT: E 391 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6277 (mp10) REVERT: E 392 ARG cc_start: 0.7588 (mpt-90) cc_final: 0.7318 (mtm110) REVERT: E 406 GLU cc_start: 0.7428 (mp0) cc_final: 0.6916 (mp0) REVERT: E 439 LEU cc_start: 0.8998 (mt) cc_final: 0.8678 (mp) REVERT: E 466 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: E 532 HIS cc_start: 0.8679 (t-90) cc_final: 0.8428 (t70) REVERT: E 544 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6910 (tt0) REVERT: E 671 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8371 (mm) REVERT: E 764 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7885 (pt0) REVERT: E 995 GLU cc_start: 0.7654 (tt0) cc_final: 0.7321 (tm-30) REVERT: E 996 VAL cc_start: 0.7515 (m) cc_final: 0.7167 (p) REVERT: E 997 LYS cc_start: 0.7024 (mmtt) cc_final: 0.6669 (mmmt) REVERT: F 167 MET cc_start: 0.6537 (mmp) cc_final: 0.6018 (ttp) REVERT: F 187 ASN cc_start: 0.8670 (t0) cc_final: 0.7865 (t0) REVERT: F 226 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.6515 (mt) REVERT: F 240 HIS cc_start: 0.6772 (p90) cc_final: 0.6127 (p90) REVERT: F 723 ASN cc_start: 0.8115 (t0) cc_final: 0.7874 (m-40) REVERT: F 801 HIS cc_start: 0.7106 (m-70) cc_final: 0.6901 (m90) REVERT: F 938 CYS cc_start: 0.7078 (m) cc_final: 0.6804 (m) REVERT: D 263 ASP cc_start: 0.7476 (t0) cc_final: 0.6822 (p0) REVERT: D 344 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: D 550 HIS cc_start: 0.8273 (p-80) cc_final: 0.7955 (p90) REVERT: D 580 TYR cc_start: 0.8606 (p90) cc_final: 0.8086 (p90) REVERT: D 593 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: D 736 HIS cc_start: 0.4810 (OUTLIER) cc_final: 0.4299 (p-80) REVERT: D 742 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7608 (m) REVERT: D 825 ARG cc_start: 0.8699 (ptt180) cc_final: 0.8126 (ptt-90) REVERT: D 922 TRP cc_start: 0.8436 (m100) cc_final: 0.8106 (m100) REVERT: D 1004 SER cc_start: 0.8796 (t) cc_final: 0.8010 (p) REVERT: C 56 LYS cc_start: 0.8108 (tttt) cc_final: 0.7580 (mmtt) REVERT: C 90 LYS cc_start: 0.8939 (tttp) cc_final: 0.8689 (tttp) REVERT: C 126 ASP cc_start: 0.9049 (t70) cc_final: 0.8848 (t0) outliers start: 71 outliers final: 55 residues processed: 276 average time/residue: 0.1578 time to fit residues: 68.9628 Evaluate side-chains 281 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 124 HIS Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 171 LEU Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 876 ASN Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 182 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 569 HIS E 723 ASN F 177 GLN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137452 restraints weight = 28805.185| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.17 r_work: 0.3321 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 23579 Z= 0.188 Angle : 0.710 59.197 32062 Z= 0.393 Chirality : 0.045 0.576 3407 Planarity : 0.004 0.104 4125 Dihedral : 5.284 80.138 3475 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.88 % Allowed : 15.87 % Favored : 81.26 % Cbeta Deviations : 0.04 % 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: -0.60 (0.15), residues: 2934 helix: 1.91 (0.22), residues: 535 sheet: -1.31 (0.26), residues: 327 loop : -0.92 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 400 TYR 0.045 0.002 TYR D 465 PHE 0.021 0.001 PHE F 176 TRP 0.016 0.001 TRP F 922 HIS 0.012 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (23468) covalent geometry : angle 0.70118 / 0.39 (31828) SS BOND : bond 0.00644 / 0.45 ( 93) SS BOND : angle 1.43896 / 0.85 ( 186) hydrogen bonds : bond 0.03278 / 2.09 ( 765) hydrogen bonds : angle 4.73139 / 3.25 ( 2352) Misc. bond : bond 0.10958 / 5.28 ( 2) link_BETA1-4 : bond 0.00291 / 0.14 ( 3) link_BETA1-4 : angle 1.49545 / 0.70 ( 9) link_NAG-ASN : bond 0.00194 / 0.10 ( 13) link_NAG-ASN : angle 1.70745 / 1.08 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.7892 (mmm160) REVERT: 2 308 ASP cc_start: 0.8784 (t0) cc_final: 0.8512 (t0) REVERT: E 299 ASP cc_start: 0.6163 (m-30) cc_final: 0.5724 (m-30) REVERT: E 391 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6265 (mp10) REVERT: E 392 ARG cc_start: 0.7586 (mpt-90) cc_final: 0.7313 (mtm110) REVERT: E 406 GLU cc_start: 0.7410 (mp0) cc_final: 0.6897 (mp0) REVERT: E 439 LEU cc_start: 0.8987 (mt) cc_final: 0.8669 (mp) REVERT: E 466 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: E 532 HIS cc_start: 0.8669 (t-90) cc_final: 0.8419 (t70) REVERT: E 544 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6911 (tt0) REVERT: E 671 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8364 (mm) REVERT: E 764 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7884 (pt0) REVERT: E 855 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7294 (ttt) REVERT: E 995 GLU cc_start: 0.7644 (tt0) cc_final: 0.7315 (tm-30) REVERT: E 996 VAL cc_start: 0.7508 (m) cc_final: 0.7162 (p) REVERT: E 997 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6676 (mmmt) REVERT: F 167 MET cc_start: 0.6503 (mmp) cc_final: 0.6009 (ttp) REVERT: F 187 ASN cc_start: 0.8659 (t0) cc_final: 0.7851 (t0) REVERT: F 226 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6511 (mt) REVERT: F 240 HIS cc_start: 0.6759 (p90) cc_final: 0.6126 (p90) REVERT: F 723 ASN cc_start: 0.8097 (t0) cc_final: 0.7861 (m-40) REVERT: F 801 HIS cc_start: 0.7107 (m-70) cc_final: 0.6906 (m90) REVERT: F 938 CYS cc_start: 0.7041 (m) cc_final: 0.6767 (m) REVERT: D 344 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: D 550 HIS cc_start: 0.8255 (p-80) cc_final: 0.7942 (p90) REVERT: D 580 TYR cc_start: 0.8584 (p90) cc_final: 0.8062 (p90) REVERT: D 593 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: D 736 HIS cc_start: 0.4816 (OUTLIER) cc_final: 0.4299 (p-80) REVERT: D 742 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7604 (m) REVERT: D 825 ARG cc_start: 0.8665 (ptt180) cc_final: 0.8086 (ptt-90) REVERT: D 922 TRP cc_start: 0.8380 (m100) cc_final: 0.7789 (m100) REVERT: D 1004 SER cc_start: 0.8773 (t) cc_final: 0.8000 (p) REVERT: C 56 LYS cc_start: 0.8092 (tttt) cc_final: 0.7574 (mmtt) REVERT: C 126 ASP cc_start: 0.9015 (t70) cc_final: 0.8808 (t0) REVERT: G 90 GLU cc_start: 0.8710 (tp30) cc_final: 0.8482 (tp30) outliers start: 70 outliers final: 56 residues processed: 268 average time/residue: 0.1551 time to fit residues: 66.5668 Evaluate side-chains 280 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 124 HIS Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 171 LEU Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 855 MET Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 279 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 216 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 569 HIS E 723 ASN F 611 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.177420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139675 restraints weight = 28902.849| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.11 r_work: 0.3326 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 23579 Z= 0.188 Angle : 0.710 59.197 32062 Z= 0.393 Chirality : 0.045 0.576 3407 Planarity : 0.004 0.104 4125 Dihedral : 5.284 80.138 3475 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 15.91 % Favored : 81.34 % Cbeta Deviations : 0.04 % 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: -0.60 (0.15), residues: 2934 helix: 1.91 (0.22), residues: 535 sheet: -1.31 (0.26), residues: 327 loop : -0.92 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 400 TYR 0.045 0.002 TYR D 465 PHE 0.021 0.001 PHE F 176 TRP 0.016 0.001 TRP F 922 HIS 0.012 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (23468) covalent geometry : angle 0.70118 / 0.39 (31828) SS BOND : bond 0.00644 / 0.45 ( 93) SS BOND : angle 1.43896 / 0.85 ( 186) hydrogen bonds : bond 0.03278 / 2.09 ( 765) hydrogen bonds : angle 4.73139 / 3.25 ( 2352) Misc. bond : bond 0.10958 / 5.28 ( 2) link_BETA1-4 : bond 0.00291 / 0.14 ( 3) link_BETA1-4 : angle 1.49545 / 0.70 ( 9) link_NAG-ASN : bond 0.00194 / 0.10 ( 13) link_NAG-ASN : angle 1.70745 / 1.08 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6912.07 seconds wall clock time: 118 minutes 41.73 seconds (7121.73 seconds total)