Starting phenix.real_space_refine on Fri Sep 19 04:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmp_38485/09_2025/8xmp_38485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmp_38485/09_2025/8xmp_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_38485/09_2025/8xmp_38485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmp_38485/09_2025/8xmp_38485.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmp_38485/09_2025/8xmp_38485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmp_38485/09_2025/8xmp_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-2.0-5805/lib/python3.9/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, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 4.79, 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: 1.66 Conformation dependent library (CDL) restraints added in 990.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.20 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: 4.66 Time building geometry restraints manager: 2.10 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 2.510 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 2.510 nonbonded pdb=" O MET F 786 " pdb="CA CA F1107 " model vdw 2.168 2.510 nonbonded pdb=" OD1 ASP F 749 " pdb="CA CA F1107 " model vdw 2.182 2.510 ... (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: 4.320 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: 0.060 Set scattering table: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 aren 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 covalent geometry : bond 0.00308 (23468) covalent geometry : angle 0.52185 (31828) SS BOND : bond 0.00324 ( 93) SS BOND : angle 0.93970 ( 186) hydrogen bonds : bond 0.21931 ( 765) hydrogen bonds : angle 8.32673 ( 2352) Misc. bond : bond 0.09347 ( 2) link_BETA1-4 : bond 0.00352 ( 3) link_BETA1-4 : angle 1.25924 ( 9) link_NAG-ASN : bond 0.00237 ( 13) link_NAG-ASN : angle 1.15704 ( 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 : 0.875 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: 0.1716 time to fit residues: 128.5575 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 : 0.852 ------------------------------------------------------------------------------- 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: 0.3980 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.181354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145979 restraints weight = 29178.773| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.23 r_work: 0.3365 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 23579 Z= 0.165 Angle : 0.582 10.172 32062 Z= 0.304 Chirality : 0.046 0.692 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.966 78.533 3476 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 1.60 % Allowed : 8.59 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.15), residues: 2934 helix: 1.87 (0.23), residues: 532 sheet: -0.91 (0.25), residues: 397 loop : -0.87 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 412 TYR 0.019 0.001 TYR 2 183 PHE 0.014 0.001 PHE 2 300 TRP 0.020 0.001 TRP D 922 HIS 0.008 0.001 HIS F 495 Details of bonding type rmsd covalent geometry : bond 0.00394 (23468) covalent geometry : angle 0.57142 (31828) SS BOND : bond 0.00345 ( 93) SS BOND : angle 1.20056 ( 186) hydrogen bonds : bond 0.04146 ( 765) hydrogen bonds : angle 5.52346 ( 2352) Misc. bond : bond 0.10415 ( 2) link_BETA1-4 : bond 0.00098 ( 3) link_BETA1-4 : angle 1.16320 ( 9) link_NAG-ASN : bond 0.00433 ( 13) link_NAG-ASN : angle 2.12964 ( 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 322 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7771 (mmm160) REVERT: 2 308 ASP cc_start: 0.8403 (t0) cc_final: 0.8141 (t0) REVERT: 2 337 GLN cc_start: 0.8218 (tt0) cc_final: 0.7912 (mt0) REVERT: E 299 ASP cc_start: 0.6089 (m-30) cc_final: 0.5716 (m-30) REVERT: E 466 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5970 (pm20) REVERT: E 532 HIS cc_start: 0.8568 (t-90) cc_final: 0.8336 (t70) REVERT: E 544 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7056 (tt0) REVERT: E 615 GLU cc_start: 0.7809 (mp0) cc_final: 0.7472 (mp0) REVERT: E 671 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8060 (mm) REVERT: E 745 ASP cc_start: 0.8670 (p0) cc_final: 0.8221 (p0) REVERT: E 764 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7751 (pt0) REVERT: E 891 ASP cc_start: 0.8492 (t0) cc_final: 0.8237 (t0) REVERT: E 938 CYS cc_start: 0.6598 (m) cc_final: 0.6281 (m) REVERT: E 970 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7455 (mp) REVERT: E 995 GLU cc_start: 0.7313 (tt0) cc_final: 0.6727 (tm-30) REVERT: E 997 LYS cc_start: 0.6746 (mmtt) cc_final: 0.5989 (mmtt) REVERT: F 167 MET cc_start: 0.6075 (mmp) cc_final: 0.5637 (ttp) REVERT: F 187 ASN cc_start: 0.8738 (t0) cc_final: 0.8074 (t0) REVERT: F 240 HIS cc_start: 0.6588 (p90) cc_final: 0.5850 (p90) REVERT: F 346 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7042 (ptmm) REVERT: F 352 LYS cc_start: 0.7547 (tttm) cc_final: 0.7004 (tmtt) REVERT: F 541 TRP cc_start: 0.8589 (m100) cc_final: 0.8273 (m100) REVERT: F 649 MET cc_start: 0.8280 (mtm) cc_final: 0.8019 (mtt) REVERT: F 723 ASN cc_start: 0.7971 (t0) cc_final: 0.7765 (m-40) REVERT: F 914 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7867 (mp) REVERT: F 922 TRP cc_start: 0.8207 (m100) cc_final: 0.7676 (m100) REVERT: D 622 GLN cc_start: 0.8532 (tp40) cc_final: 0.8228 (tp40) REVERT: D 740 TRP cc_start: 0.8305 (m100) cc_final: 0.8085 (m100) REVERT: D 825 ARG cc_start: 0.8580 (ptt180) cc_final: 0.8049 (ptt-90) REVERT: D 922 TRP cc_start: 0.8307 (m100) cc_final: 0.8067 (m100) REVERT: G 14 LEU cc_start: 0.8732 (tp) cc_final: 0.8387 (tp) outliers start: 39 outliers final: 20 residues processed: 306 average time/residue: 0.1639 time to fit residues: 78.4539 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 : 0.679 ------------------------------------------------------------------------------- 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 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 960 LEU 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: 3.9990 chunk 273 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 239 optimal weight: 0.0970 chunk 40 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140331 restraints weight = 29081.642| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.30 r_work: 0.3349 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 23579 Z= 0.161 Angle : 0.549 9.154 32062 Z= 0.287 Chirality : 0.044 0.164 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.748 79.804 3475 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 11.47 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 2934 helix: 1.88 (0.23), residues: 531 sheet: -1.11 (0.26), residues: 363 loop : -0.90 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 376 TYR 0.017 0.001 TYR 2 183 PHE 0.013 0.001 PHE 2 300 TRP 0.015 0.001 TRP F 796 HIS 0.009 0.001 HIS E 550 Details of bonding type rmsd covalent geometry : bond 0.00386 (23468) covalent geometry : angle 0.54091 (31828) SS BOND : bond 0.00320 ( 93) SS BOND : angle 1.01764 ( 186) hydrogen bonds : bond 0.03704 ( 765) hydrogen bonds : angle 5.09129 ( 2352) Misc. bond : bond 0.10959 ( 2) link_BETA1-4 : bond 0.00354 ( 3) link_BETA1-4 : angle 1.36869 ( 9) link_NAG-ASN : bond 0.00206 ( 13) link_NAG-ASN : angle 1.93308 ( 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 305 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 90 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7168 (p) REVERT: 2 202 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7906 (mmm160) REVERT: 2 308 ASP cc_start: 0.8715 (t0) cc_final: 0.8372 (t0) REVERT: 2 337 GLN cc_start: 0.8533 (tt0) cc_final: 0.8031 (mt0) REVERT: E 299 ASP cc_start: 0.6144 (m-30) cc_final: 0.5740 (m-30) REVERT: E 376 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7328 (ttp-110) REVERT: E 406 GLU cc_start: 0.7577 (mp0) cc_final: 0.6899 (mm-30) REVERT: E 466 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: E 532 HIS cc_start: 0.8638 (t-90) cc_final: 0.8389 (t70) REVERT: E 544 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7130 (tt0) REVERT: E 615 GLU cc_start: 0.7945 (mp0) cc_final: 0.7553 (mp0) REVERT: E 671 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8171 (mm) REVERT: E 745 ASP cc_start: 0.8854 (p0) cc_final: 0.8296 (p0) REVERT: E 764 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7747 (pt0) REVERT: E 820 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8134 (mt-10) REVERT: E 938 CYS cc_start: 0.6808 (m) cc_final: 0.6497 (m) REVERT: E 970 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7418 (mp) REVERT: E 995 GLU cc_start: 0.7395 (tt0) cc_final: 0.7017 (tm-30) REVERT: F 167 MET cc_start: 0.6271 (mmp) cc_final: 0.5790 (ttp) REVERT: F 187 ASN cc_start: 0.8703 (t0) cc_final: 0.8078 (t0) REVERT: F 240 HIS cc_start: 0.6666 (p90) cc_final: 0.5947 (p90) REVERT: F 336 GLN cc_start: 0.7847 (mp-120) cc_final: 0.7641 (mp10) REVERT: F 649 MET cc_start: 0.8405 (mtm) cc_final: 0.8177 (mtt) REVERT: F 723 ASN cc_start: 0.8158 (t0) cc_final: 0.7902 (m-40) REVERT: F 801 HIS cc_start: 0.6945 (m-70) cc_final: 0.6683 (m90) REVERT: F 835 CYS cc_start: 0.6423 (m) cc_final: 0.6184 (m) REVERT: F 914 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7914 (mp) REVERT: F 922 TRP cc_start: 0.8144 (m100) cc_final: 0.7726 (m-10) REVERT: F 938 CYS cc_start: 0.6766 (m) cc_final: 0.6519 (m) REVERT: D 263 ASP cc_start: 0.7922 (t70) cc_final: 0.7384 (p0) REVERT: D 550 HIS cc_start: 0.8201 (p-80) cc_final: 0.7855 (p90) REVERT: D 825 ARG cc_start: 0.8738 (ptt180) cc_final: 0.8123 (ptt-90) REVERT: D 922 TRP cc_start: 0.8499 (m100) cc_final: 0.8202 (m100) REVERT: D 964 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: D 1004 SER cc_start: 0.8898 (t) cc_final: 0.8046 (p) REVERT: C 56 LYS cc_start: 0.8188 (tttt) cc_final: 0.7605 (mmtt) REVERT: C 126 ASP cc_start: 0.9034 (t70) cc_final: 0.8789 (t0) REVERT: G 14 LEU cc_start: 0.8845 (tp) cc_final: 0.8558 (tp) outliers start: 55 outliers final: 29 residues processed: 286 average time/residue: 0.1613 time to fit residues: 72.9404 Evaluate side-chains 256 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 CYS 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 959 ASP 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 528 LEU Chi-restraints excluded: chain F residue 640 LYS 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 959 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 281 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 123 optimal weight: 0.0000 chunk 207 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS D 964 GLN G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.180571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141893 restraints weight = 28864.640| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.14 r_work: 0.3378 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 23579 Z= 0.124 Angle : 0.511 9.272 32062 Z= 0.268 Chirality : 0.043 0.324 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.491 78.905 3475 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 2.30 % Allowed : 12.66 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 2934 helix: 2.05 (0.23), residues: 533 sheet: -1.09 (0.26), residues: 340 loop : -0.87 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 318 TYR 0.015 0.001 TYR 2 183 PHE 0.011 0.001 PHE 2 300 TRP 0.015 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 Details of bonding type rmsd covalent geometry : bond 0.00296 (23468) covalent geometry : angle 0.50411 (31828) SS BOND : bond 0.00259 ( 93) SS BOND : angle 0.90268 ( 186) hydrogen bonds : bond 0.03248 ( 765) hydrogen bonds : angle 4.79847 ( 2352) Misc. bond : bond 0.09240 ( 2) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.32940 ( 9) link_NAG-ASN : bond 0.00283 ( 13) link_NAG-ASN : angle 1.73734 ( 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 300 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.7912 (mmm160) REVERT: 2 308 ASP cc_start: 0.8663 (t0) cc_final: 0.8325 (t0) REVERT: E 299 ASP cc_start: 0.6098 (m-30) cc_final: 0.5694 (m-30) REVERT: E 406 GLU cc_start: 0.7559 (mp0) cc_final: 0.6814 (mm-30) REVERT: E 408 ASP cc_start: 0.7954 (t0) cc_final: 0.7544 (t0) REVERT: E 466 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5999 (pm20) REVERT: E 532 HIS cc_start: 0.8578 (t-90) cc_final: 0.8344 (t70) REVERT: E 544 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7053 (tt0) REVERT: E 615 GLU cc_start: 0.7947 (mp0) cc_final: 0.7544 (mp0) REVERT: E 671 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8222 (mm) REVERT: E 745 ASP cc_start: 0.8835 (p0) cc_final: 0.8244 (p0) REVERT: E 764 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7811 (pt0) REVERT: E 820 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8114 (mt-10) REVERT: E 855 MET cc_start: 0.6773 (tpp) cc_final: 0.6451 (ttm) REVERT: E 938 CYS cc_start: 0.6739 (m) cc_final: 0.6513 (m) REVERT: E 995 GLU cc_start: 0.7539 (tt0) cc_final: 0.7136 (tm-30) REVERT: F 167 MET cc_start: 0.6256 (mmp) cc_final: 0.5788 (ttp) REVERT: F 187 ASN cc_start: 0.8660 (t0) cc_final: 0.8047 (t0) REVERT: F 240 HIS cc_start: 0.6595 (p90) cc_final: 0.6063 (p90) REVERT: F 723 ASN cc_start: 0.8113 (t0) cc_final: 0.7867 (m-40) REVERT: F 801 HIS cc_start: 0.6984 (m-70) cc_final: 0.6750 (m90) REVERT: F 835 CYS cc_start: 0.6515 (m) cc_final: 0.6287 (m) REVERT: F 922 TRP cc_start: 0.8076 (m100) cc_final: 0.7638 (m-10) REVERT: F 938 CYS cc_start: 0.6995 (m) cc_final: 0.6726 (m) REVERT: D 344 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: D 742 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6975 (m) REVERT: D 825 ARG cc_start: 0.8659 (ptt180) cc_final: 0.8128 (ptt-90) REVERT: D 922 TRP cc_start: 0.8546 (m100) cc_final: 0.8256 (m100) REVERT: D 1004 SER cc_start: 0.8743 (t) cc_final: 0.7998 (p) REVERT: C 56 LYS cc_start: 0.8165 (tttt) cc_final: 0.7618 (mmtt) REVERT: G 14 LEU cc_start: 0.8781 (tp) cc_final: 0.8514 (tp) outliers start: 56 outliers final: 34 residues processed: 282 average time/residue: 0.1629 time to fit residues: 73.1321 Evaluate side-chains 257 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 259 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 959 ASP 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 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 959 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 273 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 470 ILE Chi-restraints excluded: chain D residue 481 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 257 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 964 GLN G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138450 restraints weight = 28916.407| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.29 r_work: 0.3322 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 23579 Z= 0.183 Angle : 0.542 8.952 32062 Z= 0.283 Chirality : 0.044 0.227 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.460 78.985 3475 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.84 % Allowed : 12.82 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2934 helix: 1.86 (0.23), residues: 535 sheet: -1.17 (0.26), residues: 335 loop : -0.88 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 376 TYR 0.015 0.001 TYR 2 239 PHE 0.013 0.001 PHE 2 280 TRP 0.011 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 Details of bonding type rmsd covalent geometry : bond 0.00443 (23468) covalent geometry : angle 0.53220 (31828) SS BOND : bond 0.00358 ( 93) SS BOND : angle 1.17678 ( 186) hydrogen bonds : bond 0.03323 ( 765) hydrogen bonds : angle 4.81517 ( 2352) Misc. bond : bond 0.12077 ( 2) link_BETA1-4 : bond 0.00409 ( 3) link_BETA1-4 : angle 1.47813 ( 9) link_NAG-ASN : bond 0.00198 ( 13) link_NAG-ASN : angle 1.75779 ( 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 304 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.7914 (mmm160) REVERT: 2 308 ASP cc_start: 0.8709 (t0) cc_final: 0.8380 (t0) REVERT: E 299 ASP cc_start: 0.6198 (m-30) cc_final: 0.5795 (m-30) REVERT: E 406 GLU cc_start: 0.7435 (mp0) cc_final: 0.6725 (mm-30) REVERT: E 408 ASP cc_start: 0.7963 (t0) cc_final: 0.7563 (t0) REVERT: E 466 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: E 532 HIS cc_start: 0.8596 (t-90) cc_final: 0.8335 (t70) REVERT: E 544 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7040 (tt0) REVERT: E 615 GLU cc_start: 0.7969 (mp0) cc_final: 0.7503 (mp0) REVERT: E 671 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8259 (mm) REVERT: E 745 ASP cc_start: 0.8875 (p0) cc_final: 0.8607 (p0) REVERT: E 764 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7844 (pt0) REVERT: E 820 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8185 (mt-10) REVERT: E 995 GLU cc_start: 0.7512 (tt0) cc_final: 0.7150 (tm-30) REVERT: F 167 MET cc_start: 0.6286 (mmp) cc_final: 0.5840 (ttp) REVERT: F 187 ASN cc_start: 0.8638 (t0) cc_final: 0.7996 (t0) REVERT: F 240 HIS cc_start: 0.6716 (p90) cc_final: 0.6067 (p90) REVERT: F 253 ASP cc_start: 0.7861 (m-30) cc_final: 0.7612 (m-30) REVERT: F 360 ASP cc_start: 0.8433 (m-30) cc_final: 0.8145 (m-30) REVERT: F 723 ASN cc_start: 0.8120 (t0) cc_final: 0.7862 (m-40) REVERT: F 801 HIS cc_start: 0.7043 (m170) cc_final: 0.6825 (m90) REVERT: F 835 CYS cc_start: 0.6786 (m) cc_final: 0.6576 (m) REVERT: F 903 TRP cc_start: 0.8255 (m-10) cc_final: 0.7793 (m100) REVERT: F 922 TRP cc_start: 0.8126 (m100) cc_final: 0.7777 (m100) REVERT: F 938 CYS cc_start: 0.6956 (m) cc_final: 0.6689 (m) REVERT: D 263 ASP cc_start: 0.7497 (t0) cc_final: 0.6950 (p0) REVERT: D 344 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: D 550 HIS cc_start: 0.8198 (p-80) cc_final: 0.7878 (p90) REVERT: D 742 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7081 (m) REVERT: D 825 ARG cc_start: 0.8667 (ptt180) cc_final: 0.8049 (ptt-90) REVERT: D 1004 SER cc_start: 0.8854 (t) cc_final: 0.8082 (p) REVERT: C 56 LYS cc_start: 0.8174 (tttt) cc_final: 0.7657 (mmtt) REVERT: C 126 ASP cc_start: 0.9030 (t70) cc_final: 0.8791 (t0) outliers start: 69 outliers final: 48 residues processed: 287 average time/residue: 0.1662 time to fit residues: 75.7261 Evaluate side-chains 269 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 2 residue 324 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 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 467 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 760 LEU Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 959 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 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 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL 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 964 GLN Chi-restraints excluded: chain C residue 1 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 242 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 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 241 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137029 restraints weight = 29003.705| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.17 r_work: 0.3372 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 23579 Z= 0.129 Angle : 0.510 9.165 32062 Z= 0.267 Chirality : 0.043 0.201 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.284 77.915 3475 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 2.88 % Allowed : 13.81 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 2934 helix: 1.97 (0.23), residues: 535 sheet: -1.21 (0.26), residues: 343 loop : -0.84 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 392 TYR 0.014 0.001 TYR 2 239 PHE 0.011 0.001 PHE 2 300 TRP 0.011 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 Details of bonding type rmsd covalent geometry : bond 0.00310 (23468) covalent geometry : angle 0.50282 (31828) SS BOND : bond 0.00265 ( 93) SS BOND : angle 1.00903 ( 186) hydrogen bonds : bond 0.03083 ( 765) hydrogen bonds : angle 4.65689 ( 2352) Misc. bond : bond 0.09741 ( 2) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 1.34733 ( 9) link_NAG-ASN : bond 0.00183 ( 13) link_NAG-ASN : angle 1.61153 ( 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 299 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.7872 (mmm160) REVERT: 2 308 ASP cc_start: 0.8679 (t0) cc_final: 0.8328 (t0) REVERT: E 299 ASP cc_start: 0.6082 (m-30) cc_final: 0.5656 (m-30) REVERT: E 358 ASN cc_start: 0.6823 (m-40) cc_final: 0.6601 (m-40) REVERT: E 406 GLU cc_start: 0.7426 (mp0) cc_final: 0.6684 (mm-30) REVERT: E 408 ASP cc_start: 0.7881 (t0) cc_final: 0.7504 (t0) REVERT: E 466 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6085 (pm20) REVERT: E 532 HIS cc_start: 0.8591 (t-90) cc_final: 0.8317 (t70) REVERT: E 544 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7034 (tt0) REVERT: E 671 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8278 (mm) REVERT: E 745 ASP cc_start: 0.8835 (p0) cc_final: 0.8560 (p0) REVERT: E 764 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7809 (pt0) REVERT: E 820 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8163 (mt-10) REVERT: E 855 MET cc_start: 0.7143 (ttm) cc_final: 0.6719 (ttm) REVERT: E 995 GLU cc_start: 0.7580 (tt0) cc_final: 0.7138 (tm-30) REVERT: F 167 MET cc_start: 0.6299 (mmp) cc_final: 0.5775 (ttp) REVERT: F 240 HIS cc_start: 0.6695 (p90) cc_final: 0.6134 (p90) REVERT: F 723 ASN cc_start: 0.8097 (t0) cc_final: 0.7831 (m-40) REVERT: F 801 HIS cc_start: 0.7060 (m170) cc_final: 0.6836 (m90) REVERT: F 922 TRP cc_start: 0.8054 (m100) cc_final: 0.7730 (m100) REVERT: F 938 CYS cc_start: 0.6858 (m) cc_final: 0.6586 (m) REVERT: D 344 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: D 550 HIS cc_start: 0.8220 (p-80) cc_final: 0.7931 (p90) REVERT: D 742 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7057 (m) REVERT: D 825 ARG cc_start: 0.8617 (ptt180) cc_final: 0.8078 (ptt-90) REVERT: D 1004 SER cc_start: 0.8718 (t) cc_final: 0.8040 (p) REVERT: C 56 LYS cc_start: 0.8092 (tttt) cc_final: 0.7563 (mmtt) REVERT: G 14 LEU cc_start: 0.8657 (tp) cc_final: 0.8284 (tp) outliers start: 70 outliers final: 47 residues processed: 284 average time/residue: 0.1541 time to fit residues: 69.2550 Evaluate side-chains 265 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 959 ASP 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 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS 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 796 TRP Chi-restraints excluded: chain F residue 959 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 241 GLN 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 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: 0.8980 chunk 151 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 129 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN F 648 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139209 restraints weight = 29059.025| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.23 r_work: 0.3346 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 23579 Z= 0.141 Angle : 0.514 8.805 32062 Z= 0.269 Chirality : 0.043 0.248 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.198 77.573 3475 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 2.88 % Allowed : 14.59 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 2934 helix: 1.96 (0.23), residues: 537 sheet: -1.19 (0.26), residues: 343 loop : -0.84 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 392 TYR 0.014 0.001 TYR 2 239 PHE 0.012 0.001 PHE 2 300 TRP 0.012 0.001 TRP D 243 HIS 0.008 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00339 (23468) covalent geometry : angle 0.50686 (31828) SS BOND : bond 0.00279 ( 93) SS BOND : angle 0.97563 ( 186) hydrogen bonds : bond 0.03064 ( 765) hydrogen bonds : angle 4.62084 ( 2352) Misc. bond : bond 0.10075 ( 2) link_BETA1-4 : bond 0.00359 ( 3) link_BETA1-4 : angle 1.39402 ( 9) link_NAG-ASN : bond 0.00176 ( 13) link_NAG-ASN : angle 1.60399 ( 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 302 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.7895 (mmm160) REVERT: 2 308 ASP cc_start: 0.8756 (t0) cc_final: 0.8401 (t0) REVERT: E 299 ASP cc_start: 0.6131 (m-30) cc_final: 0.5704 (m-30) REVERT: E 376 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7413 (ttp-110) REVERT: E 406 GLU cc_start: 0.7443 (mp0) cc_final: 0.6722 (mm-30) REVERT: E 408 ASP cc_start: 0.7893 (t0) cc_final: 0.7524 (t0) REVERT: E 466 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6190 (pm20) REVERT: E 532 HIS cc_start: 0.8575 (t-90) cc_final: 0.8303 (t70) REVERT: E 544 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7005 (tt0) REVERT: E 671 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8295 (mm) REVERT: E 745 ASP cc_start: 0.8877 (p0) cc_final: 0.8589 (p0) REVERT: E 764 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7810 (pt0) REVERT: E 820 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8187 (mt-10) REVERT: E 995 GLU cc_start: 0.7584 (tt0) cc_final: 0.7137 (tm-30) REVERT: F 167 MET cc_start: 0.6277 (mmp) cc_final: 0.5798 (ttp) REVERT: F 240 HIS cc_start: 0.6758 (p90) cc_final: 0.6096 (p90) REVERT: F 645 ILE cc_start: 0.7827 (mm) cc_final: 0.7447 (pt) REVERT: F 723 ASN cc_start: 0.8109 (t0) cc_final: 0.7851 (m-40) REVERT: F 801 HIS cc_start: 0.7098 (m170) cc_final: 0.6891 (m90) REVERT: F 922 TRP cc_start: 0.8097 (m100) cc_final: 0.7787 (m100) REVERT: F 938 CYS cc_start: 0.6921 (m) cc_final: 0.6648 (m) REVERT: D 263 ASP cc_start: 0.7418 (t0) cc_final: 0.6728 (p0) REVERT: D 344 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: D 550 HIS cc_start: 0.8221 (p-80) cc_final: 0.7936 (p90) REVERT: D 736 HIS cc_start: 0.4810 (OUTLIER) cc_final: 0.4263 (p-80) REVERT: D 742 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7177 (m) REVERT: D 825 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8127 (ptt-90) REVERT: D 1004 SER cc_start: 0.8694 (t) cc_final: 0.8007 (p) REVERT: C 56 LYS cc_start: 0.8110 (tttt) cc_final: 0.7583 (mmtt) REVERT: G 14 LEU cc_start: 0.8768 (tp) cc_final: 0.8507 (tp) outliers start: 70 outliers final: 50 residues processed: 284 average time/residue: 0.1645 time to fit residues: 73.8834 Evaluate side-chains 273 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 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 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 959 ASP 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 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 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 959 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 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 1 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 207 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 217 optimal weight: 0.0470 chunk 246 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138732 restraints weight = 28890.832| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.32 r_work: 0.3305 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 23579 Z= 0.180 Angle : 0.541 8.923 32062 Z= 0.283 Chirality : 0.044 0.218 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.236 78.315 3475 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 2.92 % Allowed : 14.80 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 2934 helix: 1.85 (0.22), residues: 537 sheet: -1.22 (0.26), residues: 343 loop : -0.87 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 392 TYR 0.020 0.002 TYR D 465 PHE 0.014 0.001 PHE 2 280 TRP 0.012 0.001 TRP C 14 HIS 0.007 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00436 (23468) covalent geometry : angle 0.53302 (31828) SS BOND : bond 0.00346 ( 93) SS BOND : angle 1.09393 ( 186) hydrogen bonds : bond 0.03191 ( 765) hydrogen bonds : angle 4.70133 ( 2352) Misc. bond : bond 0.11681 ( 2) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.48239 ( 9) link_NAG-ASN : bond 0.00197 ( 13) link_NAG-ASN : angle 1.69144 ( 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 303 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7798 (mmm160) REVERT: 2 308 ASP cc_start: 0.8539 (t0) cc_final: 0.8274 (t0) REVERT: E 299 ASP cc_start: 0.6157 (m-30) cc_final: 0.5735 (m-30) REVERT: E 406 GLU cc_start: 0.7390 (mp0) cc_final: 0.6705 (mm-30) REVERT: E 408 ASP cc_start: 0.7870 (t0) cc_final: 0.7502 (t0) REVERT: E 466 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6270 (pm20) REVERT: E 532 HIS cc_start: 0.8548 (t-90) cc_final: 0.8299 (t70) REVERT: E 544 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7082 (tt0) REVERT: E 671 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8324 (mm) REVERT: E 745 ASP cc_start: 0.8775 (p0) cc_final: 0.8479 (p0) REVERT: E 764 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7800 (pt0) REVERT: E 855 MET cc_start: 0.7208 (ttm) cc_final: 0.6832 (ttm) REVERT: E 995 GLU cc_start: 0.7573 (tt0) cc_final: 0.7295 (tm-30) REVERT: F 167 MET cc_start: 0.6282 (mmp) cc_final: 0.5885 (ttp) REVERT: F 187 ASN cc_start: 0.8588 (t0) cc_final: 0.7763 (t0) REVERT: F 226 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6568 (mt) REVERT: F 240 HIS cc_start: 0.6667 (p90) cc_final: 0.6062 (p90) REVERT: F 645 ILE cc_start: 0.7749 (mm) cc_final: 0.7395 (pt) REVERT: F 723 ASN cc_start: 0.7965 (t0) cc_final: 0.7754 (m-40) REVERT: F 903 TRP cc_start: 0.8086 (m-10) cc_final: 0.7810 (m100) REVERT: F 922 TRP cc_start: 0.8038 (m100) cc_final: 0.7778 (m100) REVERT: F 938 CYS cc_start: 0.6567 (m) cc_final: 0.6281 (m) REVERT: D 344 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: D 550 HIS cc_start: 0.8108 (p-80) cc_final: 0.7819 (p90) REVERT: D 736 HIS cc_start: 0.4848 (OUTLIER) cc_final: 0.4277 (p-80) REVERT: D 742 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7254 (m) REVERT: D 825 ARG cc_start: 0.8526 (ptt180) cc_final: 0.7913 (ptt-90) REVERT: D 922 TRP cc_start: 0.8259 (m100) cc_final: 0.7964 (m100) REVERT: D 1004 SER cc_start: 0.8662 (t) cc_final: 0.7892 (p) REVERT: C 56 LYS cc_start: 0.7960 (tttt) cc_final: 0.7556 (mmtt) REVERT: C 126 ASP cc_start: 0.8737 (t70) cc_final: 0.8484 (t0) REVERT: G 14 LEU cc_start: 0.8739 (tp) cc_final: 0.8476 (tp) outliers start: 71 outliers final: 55 residues processed: 284 average time/residue: 0.1537 time to fit residues: 69.4101 Evaluate side-chains 278 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL 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 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 959 ASP 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 640 LYS 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 796 TRP Chi-restraints excluded: chain F residue 959 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 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 1 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 44 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.178356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141408 restraints weight = 28982.700| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.06 r_work: 0.3347 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2831 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= 0.151 Angle : 0.529 8.883 32062 Z= 0.276 Chirality : 0.043 0.208 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.162 79.801 3475 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 2.75 % Allowed : 15.33 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 2934 helix: 1.94 (0.23), residues: 537 sheet: -1.19 (0.26), residues: 343 loop : -0.85 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 392 TYR 0.029 0.001 TYR D 465 PHE 0.012 0.001 PHE 2 300 TRP 0.012 0.001 TRP F 796 HIS 0.007 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00366 (23468) covalent geometry : angle 0.52136 (31828) SS BOND : bond 0.00299 ( 93) SS BOND : angle 1.01515 ( 186) hydrogen bonds : bond 0.03104 ( 765) hydrogen bonds : angle 4.63469 ( 2352) Misc. bond : bond 0.10287 ( 2) link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.38849 ( 9) link_NAG-ASN : bond 0.00191 ( 13) link_NAG-ASN : angle 1.62666 ( 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 292 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7879 (mmm160) REVERT: 2 308 ASP cc_start: 0.8730 (t0) cc_final: 0.8462 (t0) REVERT: E 299 ASP cc_start: 0.6172 (m-30) cc_final: 0.5754 (m-30) REVERT: E 376 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7507 (ttp-110) REVERT: E 406 GLU cc_start: 0.7352 (mp0) cc_final: 0.7067 (mp0) REVERT: E 408 ASP cc_start: 0.7920 (t0) cc_final: 0.7555 (t0) REVERT: E 466 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6192 (pm20) REVERT: E 532 HIS cc_start: 0.8556 (t-90) cc_final: 0.8314 (t70) REVERT: E 544 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7043 (tt0) REVERT: E 671 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8322 (mm) REVERT: E 745 ASP cc_start: 0.8855 (p0) cc_final: 0.8565 (p0) REVERT: E 764 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7796 (pt0) REVERT: E 855 MET cc_start: 0.7311 (ttm) cc_final: 0.6957 (ttm) REVERT: E 995 GLU cc_start: 0.7608 (tt0) cc_final: 0.7315 (tm-30) REVERT: F 167 MET cc_start: 0.6357 (mmp) cc_final: 0.5952 (ttp) REVERT: F 187 ASN cc_start: 0.8652 (t0) cc_final: 0.7851 (t0) REVERT: F 226 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.6618 (mt) REVERT: F 240 HIS cc_start: 0.6715 (p90) cc_final: 0.6055 (p90) REVERT: F 645 ILE cc_start: 0.7851 (mm) cc_final: 0.7482 (pt) REVERT: F 723 ASN cc_start: 0.8031 (t0) cc_final: 0.7823 (m-40) REVERT: F 785 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7213 (mm-30) REVERT: F 903 TRP cc_start: 0.8193 (m-10) cc_final: 0.7948 (m100) REVERT: F 922 TRP cc_start: 0.8120 (m100) cc_final: 0.7900 (m100) REVERT: F 938 CYS cc_start: 0.6855 (m) cc_final: 0.6572 (m) REVERT: D 263 ASP cc_start: 0.7393 (t0) cc_final: 0.6706 (p0) REVERT: D 344 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: D 550 HIS cc_start: 0.8201 (p-80) cc_final: 0.7905 (p90) REVERT: D 736 HIS cc_start: 0.4768 (OUTLIER) cc_final: 0.4255 (p-80) REVERT: D 742 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7278 (m) REVERT: D 825 ARG cc_start: 0.8633 (ptt180) cc_final: 0.8049 (ptt-90) REVERT: D 922 TRP cc_start: 0.8300 (m100) cc_final: 0.7964 (m100) REVERT: D 1004 SER cc_start: 0.8736 (t) cc_final: 0.7954 (p) REVERT: C 56 LYS cc_start: 0.8043 (tttt) cc_final: 0.7566 (mmtt) REVERT: G 14 LEU cc_start: 0.8747 (tp) cc_final: 0.8513 (tp) outliers start: 67 outliers final: 55 residues processed: 275 average time/residue: 0.1544 time to fit residues: 67.0964 Evaluate side-chains 271 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 171 LEU 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 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 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER 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 959 ASP 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 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL 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 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 959 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 182 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 201 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141372 restraints weight = 28858.614| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.13 r_work: 0.3342 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 23579 Z= 0.151 Angle : 0.527 8.722 32062 Z= 0.275 Chirality : 0.043 0.196 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.128 81.132 3475 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 2.79 % Allowed : 15.50 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 2934 helix: 1.94 (0.23), residues: 537 sheet: -1.25 (0.26), residues: 335 loop : -0.84 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 392 TYR 0.021 0.001 TYR D 465 PHE 0.012 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 covalent geometry : bond 0.00366 (23468) covalent geometry : angle 0.51953 (31828) SS BOND : bond 0.00294 ( 93) SS BOND : angle 0.99963 ( 186) hydrogen bonds : bond 0.03080 ( 765) hydrogen bonds : angle 4.61475 ( 2352) Misc. bond : bond 0.10192 ( 2) link_BETA1-4 : bond 0.00251 ( 3) link_BETA1-4 : angle 1.38637 ( 9) link_NAG-ASN : bond 0.00191 ( 13) link_NAG-ASN : angle 1.62448 ( 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 292 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7897 (mmm160) REVERT: 2 308 ASP cc_start: 0.8799 (t0) cc_final: 0.8530 (t0) REVERT: E 299 ASP cc_start: 0.6187 (m-30) cc_final: 0.5764 (m-30) REVERT: E 376 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7534 (ttp-110) REVERT: E 406 GLU cc_start: 0.7392 (mp0) cc_final: 0.7103 (mp0) REVERT: E 408 ASP cc_start: 0.7923 (t0) cc_final: 0.7556 (t0) REVERT: E 466 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: E 532 HIS cc_start: 0.8593 (t-90) cc_final: 0.8333 (t70) REVERT: E 544 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7052 (tt0) REVERT: E 671 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8344 (mm) REVERT: E 745 ASP cc_start: 0.8873 (p0) cc_final: 0.8599 (p0) REVERT: E 764 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7819 (pt0) REVERT: E 995 GLU cc_start: 0.7677 (tt0) cc_final: 0.7334 (tm-30) REVERT: F 167 MET cc_start: 0.6442 (mmp) cc_final: 0.5972 (ttp) REVERT: F 187 ASN cc_start: 0.8654 (t0) cc_final: 0.7855 (t0) REVERT: F 226 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.6594 (mt) REVERT: F 240 HIS cc_start: 0.6798 (p90) cc_final: 0.6122 (p90) REVERT: F 645 ILE cc_start: 0.7835 (mm) cc_final: 0.7494 (pt) REVERT: F 723 ASN cc_start: 0.8124 (t0) cc_final: 0.7883 (m-40) REVERT: F 801 HIS cc_start: 0.7236 (m170) cc_final: 0.7030 (m90) REVERT: F 913 ARG cc_start: 0.7227 (ptt90) cc_final: 0.6993 (ptt-90) REVERT: F 922 TRP cc_start: 0.8128 (m100) cc_final: 0.7903 (m100) REVERT: F 938 CYS cc_start: 0.6975 (m) cc_final: 0.6698 (m) REVERT: D 263 ASP cc_start: 0.7422 (t0) cc_final: 0.6825 (p0) REVERT: D 344 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: D 400 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7795 (ttm110) REVERT: D 548 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 550 HIS cc_start: 0.8268 (p-80) cc_final: 0.7923 (p90) REVERT: D 736 HIS cc_start: 0.4762 (OUTLIER) cc_final: 0.4241 (p-80) REVERT: D 742 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7371 (m) REVERT: D 825 ARG cc_start: 0.8669 (ptt180) cc_final: 0.8100 (ptt-90) REVERT: D 922 TRP cc_start: 0.8243 (m100) cc_final: 0.8027 (m100) REVERT: D 1004 SER cc_start: 0.8758 (t) cc_final: 0.7969 (p) REVERT: C 56 LYS cc_start: 0.8122 (tttt) cc_final: 0.7591 (mmtt) REVERT: G 14 LEU cc_start: 0.8749 (tp) cc_final: 0.8535 (tp) outliers start: 68 outliers final: 56 residues processed: 274 average time/residue: 0.1509 time to fit residues: 64.7192 Evaluate side-chains 279 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 171 LEU 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 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 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER 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 959 ASP 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 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 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 796 TRP Chi-restraints excluded: chain F residue 959 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 279 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 280 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134826 restraints weight = 28995.358| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.22 r_work: 0.3327 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 23579 Z= 0.184 Angle : 0.545 9.127 32062 Z= 0.284 Chirality : 0.044 0.208 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.193 81.678 3475 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 2.79 % Allowed : 15.54 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 2934 helix: 1.82 (0.22), residues: 538 sheet: -1.30 (0.25), residues: 343 loop : -0.86 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 392 TYR 0.018 0.002 TYR D 465 PHE 0.014 0.001 PHE 2 280 TRP 0.011 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 Details of bonding type rmsd covalent geometry : bond 0.00446 (23468) covalent geometry : angle 0.53649 (31828) SS BOND : bond 0.00356 ( 93) SS BOND : angle 1.08500 ( 186) hydrogen bonds : bond 0.03179 ( 765) hydrogen bonds : angle 4.68969 ( 2352) Misc. bond : bond 0.11542 ( 2) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 1.48667 ( 9) link_NAG-ASN : bond 0.00201 ( 13) link_NAG-ASN : angle 1.69380 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7197.97 seconds wall clock time: 123 minutes 27.97 seconds (7407.97 seconds total)