Starting phenix.real_space_refine on Sat Jul 4 03:54:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.map" model { file = "/net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asb_43811/07_2026/9asb_43811.cif" } resolution = 3.4 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= 0.002 sd= 0.042 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 P 3 5.49 5 S 103 5.16 5 Cl 2 4.86 5 C 11689 2.51 5 N 3002 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18185 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6402 Classifications: {'peptide': 804} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Chain: "R" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6449 Classifications: {'peptide': 809} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 775} Chain breaks: 2 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1928 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 4 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 Time building chain proxies: 3.89, per 1000 atoms: 0.21 Number of scatterers: 18185 At special positions: 0 Unit cell: (93.225, 121.275, 246.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 103 16.00 P 3 15.00 O 3380 8.00 N 3002 7.00 C 11689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 568 " - pdb=" SG CYS Q 582 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 585 " - pdb=" SG CYS Q 598 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 754.3 milliseconds 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4222 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 46.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 84 Processing helix chain 'Q' and resid 103 through 115 Processing helix chain 'Q' and resid 115 through 123 Processing helix chain 'Q' and resid 146 through 158 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.507A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.569A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 262 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 356 Processing helix chain 'Q' and resid 400 through 404 removed outlier: 3.733A pdb=" N VAL Q 404 " --> pdb=" O ILE Q 401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 451 through 455 removed outlier: 3.991A pdb=" N VAL Q 455 " --> pdb=" O ILE Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 456 through 466 Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.703A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 668 No H-bonds generated for 'chain 'Q' and resid 666 through 668' Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.609A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 702 through 708 Processing helix chain 'Q' and resid 722 through 746 removed outlier: 3.770A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 793 Processing helix chain 'Q' and resid 798 through 827 removed outlier: 6.045A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 831 through 862 removed outlier: 3.965A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 4.012A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) Processing helix chain 'Q' and resid 868 through 873 Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 115 Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.842A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.510A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 removed outlier: 3.665A pdb=" N ALA R 194 " --> pdb=" O ASP R 190 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR R 195 " --> pdb=" O GLU R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.577A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 272 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 4.531A pdb=" N SER R 301 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 removed outlier: 3.615A pdb=" N VAL R 404 " --> pdb=" O ILE R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 451 through 455 removed outlier: 3.879A pdb=" N VAL R 455 " --> pdb=" O ILE R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 466 Processing helix chain 'R' and resid 525 through 528 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 Processing helix chain 'R' and resid 647 through 665 Processing helix chain 'R' and resid 666 through 669 removed outlier: 3.716A pdb=" N ILE R 669 " --> pdb=" O LEU R 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 666 through 669' Processing helix chain 'R' and resid 673 through 707 removed outlier: 4.413A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix Processing helix chain 'R' and resid 718 through 746 Processing helix chain 'R' and resid 769 through 794 Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 821 Processing helix chain 'R' and resid 821 through 826 Processing helix chain 'R' and resid 830 through 862 removed outlier: 3.813A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 removed outlier: 4.003A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.754A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 132 through 135 removed outlier: 3.549A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.628A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.775A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.078A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN Q 164 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 41 through 44 removed outlier: 7.144A pdb=" N ARG Q 62 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL Q 44 " --> pdb=" O CYS Q 60 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS Q 60 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 236 through 243 removed outlier: 6.438A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE Q 239 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA6, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA7, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA8, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.394A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 25 through 28 removed outlier: 6.066A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 236 through 243 removed outlier: 7.912A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE R 267 " --> pdb=" O LEU R 294 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 468 through 470 Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604 Processing sheet with id=AB7, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.430A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.180A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.006A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.975A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.071A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.691A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.971A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.315A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2487 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: 3.67 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5710 1.34 - 1.46: 4353 1.46 - 1.58: 8407 1.58 - 1.71: 3 1.71 - 1.83: 132 Bond restraints: 18605 Sorted by residual: bond pdb=" CAI Y01 Q1011 " pdb=" CAK Y01 Q1011 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O4 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" O4 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 18600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 24890 2.37 - 4.74: 282 4.74 - 7.10: 30 7.10 - 9.47: 7 9.47 - 11.84: 3 Bond angle restraints: 25212 Sorted by residual: angle pdb=" OAG Y01 Q1011 " pdb=" CAY Y01 Q1011 " pdb=" OAW Y01 Q1011 " ideal model delta sigma weight residual 123.38 111.54 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CAM Y01 Q1011 " pdb=" CAY Y01 Q1011 " pdb=" OAW Y01 Q1011 " ideal model delta sigma weight residual 111.19 122.58 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N ILE Q 305 " pdb=" CA ILE Q 305 " pdb=" C ILE Q 305 " ideal model delta sigma weight residual 112.12 108.98 3.14 8.40e-01 1.42e+00 1.39e+01 angle pdb=" N VAL R 508 " pdb=" CA VAL R 508 " pdb=" C VAL R 508 " ideal model delta sigma weight residual 112.43 109.47 2.96 9.20e-01 1.18e+00 1.04e+01 angle pdb=" CAV Y01 Q1011 " pdb=" CAZ Y01 Q1011 " pdb=" CBH Y01 Q1011 " ideal model delta sigma weight residual 116.96 126.10 -9.14 3.00e+00 1.11e-01 9.28e+00 ... (remaining 25207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10275 17.88 - 35.76: 800 35.76 - 53.64: 145 53.64 - 71.52: 32 71.52 - 89.40: 15 Dihedral angle restraints: 11267 sinusoidal: 4746 harmonic: 6521 Sorted by residual: dihedral pdb=" CA ALA A 176 " pdb=" C ALA A 176 " pdb=" N THR A 177 " pdb=" CA THR A 177 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS Q 546 " pdb=" SG CYS Q 546 " pdb=" SG CYS Q 565 " pdb=" CB CYS Q 565 " ideal model delta sinusoidal sigma weight residual -86.00 -113.79 27.79 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA PRO A 178 " pdb=" C PRO A 178 " pdb=" N GLU A 179 " pdb=" CA GLU A 179 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 11264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2269 0.053 - 0.105: 482 0.105 - 0.158: 72 0.158 - 0.211: 7 0.211 - 0.264: 1 Chirality restraints: 2831 Sorted by residual: chirality pdb=" C02 A1AF7 R1009 " pdb=" C01 A1AF7 R1009 " pdb=" C03 A1AF7 R1009 " pdb=" O01 A1AF7 R1009 " both_signs ideal model delta sigma weight residual False 2.54 2.80 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CBF Y01 Q1011 " pdb=" CAS Y01 Q1011 " pdb=" CBD Y01 Q1011 " pdb=" CBH Y01 Q1011 " both_signs ideal model delta sigma weight residual False -2.45 -2.64 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" C05 A1AF7 R1009 " pdb=" C04 A1AF7 R1009 " pdb=" CAD A1AF7 R1009 " pdb=" OAF A1AF7 R1009 " both_signs ideal model delta sigma weight residual False -2.53 -2.71 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2828 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 438 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO Q 439 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO Q 439 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 439 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 177 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.80e+00 pdb=" N PRO A 178 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.54e+00 pdb=" N PRO G 55 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.030 5.00e-02 4.00e+02 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 645 2.71 - 3.26: 18567 3.26 - 3.81: 30977 3.81 - 4.35: 39593 4.35 - 4.90: 65467 Nonbonded interactions: 155249 Sorted by model distance: nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.168 3.040 nonbonded pdb=" NE2 GLN R 253 " pdb=" OE2 GLU R 257 " model vdw 2.176 3.120 nonbonded pdb=" OD1 ASN Q 468 " pdb=" NE2 GLN Q 476 " model vdw 2.180 3.120 nonbonded pdb=" OG SER R 175 " pdb=" NH2 ARG R 185 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP R 588 " pdb=" NH2 ARG R 752 " model vdw 2.239 3.120 ... (remaining 155244 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 21 through 867 or resid 1003 or resid 1008 through 1010)) selection = (chain 'R' and (resid 21 through 124 or resid 133 through 708 or resid 719 throu \ gh 1001 or resid 1006 through 1008)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.170 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.650 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 18635 Z= 0.218 Angle : 0.671 11.841 25286 Z= 0.358 Chirality : 0.044 0.264 2831 Planarity : 0.005 0.083 3187 Dihedral : 13.475 89.404 6997 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2219 helix: 1.07 (0.17), residues: 905 sheet: -1.44 (0.27), residues: 358 loop : -0.72 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.028 0.001 TYR B 85 PHE 0.021 0.002 PHE A 74 TRP 0.019 0.002 TRP B 99 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (18605) covalent geometry : angle 0.66560 / 0.36 (25212) SS BOND : bond 0.00225 / 0.16 ( 16) SS BOND : angle 1.04295 / 0.71 ( 32) hydrogen bonds : bond 0.13527 / 9.09 ( 868) hydrogen bonds : angle 6.08816 / 4.32 ( 2487) link_BETA1-4 : bond 0.00300 / 0.20 ( 4) link_BETA1-4 : angle 1.14173 / 0.77 ( 12) link_NAG-ASN : bond 0.00249 / 0.19 ( 10) link_NAG-ASN : angle 2.41275 / 1.22 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 27 GLN cc_start: 0.7704 (tt0) cc_final: 0.7501 (tt0) REVERT: R 52 LYS cc_start: 0.8111 (mttt) cc_final: 0.7880 (mtpt) REVERT: R 263 THR cc_start: 0.8088 (p) cc_final: 0.7846 (p) REVERT: R 636 LYS cc_start: 0.7308 (mtmt) cc_final: 0.6775 (mmtm) REVERT: R 756 LEU cc_start: 0.7907 (mt) cc_final: 0.7705 (mt) REVERT: A 130 ASN cc_start: 0.7383 (m110) cc_final: 0.7140 (m110) REVERT: A 160 ILE cc_start: 0.8538 (mp) cc_final: 0.8008 (mp) REVERT: A 195 ASP cc_start: 0.6566 (t70) cc_final: 0.6317 (t0) REVERT: B 291 ASP cc_start: 0.7286 (m-30) cc_final: 0.7035 (m-30) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1430 time to fit residues: 84.9991 Evaluate side-chains 357 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.0670 chunk 212 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093997 restraints weight = 28732.285| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.63 r_work: 0.2994 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18635 Z= 0.184 Angle : 0.577 9.304 25286 Z= 0.303 Chirality : 0.044 0.224 2831 Planarity : 0.005 0.064 3187 Dihedral : 7.207 72.804 2862 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.13 % Allowed : 7.84 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2219 helix: 1.23 (0.17), residues: 906 sheet: -1.36 (0.26), residues: 363 loop : -0.67 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 185 TYR 0.016 0.002 TYR R 421 PHE 0.019 0.002 PHE A 70 TRP 0.018 0.001 TRP Q 818 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (18605) covalent geometry : angle 0.56867 / 0.30 (25212) SS BOND : bond 0.00438 / 0.34 ( 16) SS BOND : angle 1.98822 / 1.36 ( 32) hydrogen bonds : bond 0.05291 / 3.54 ( 868) hydrogen bonds : angle 4.91369 / 3.52 ( 2487) link_BETA1-4 : bond 0.00337 / 0.22 ( 4) link_BETA1-4 : angle 1.07172 / 0.71 ( 12) link_NAG-ASN : bond 0.00289 / 0.22 ( 10) link_NAG-ASN : angle 2.11771 / 1.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 389 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7464 (pp20) cc_final: 0.6821 (pp20) REVERT: Q 769 SER cc_start: 0.8506 (t) cc_final: 0.8193 (m) REVERT: R 52 LYS cc_start: 0.8168 (mttt) cc_final: 0.7761 (mtpt) REVERT: R 191 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7645 (mm-30) REVERT: R 263 THR cc_start: 0.8313 (p) cc_final: 0.8076 (p) REVERT: R 297 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6661 (tm-30) REVERT: R 636 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7129 (mmtm) REVERT: R 756 LEU cc_start: 0.8244 (mt) cc_final: 0.7964 (mt) REVERT: A 25 LYS cc_start: 0.8336 (tppt) cc_final: 0.8022 (mmmm) REVERT: A 43 ASN cc_start: 0.7709 (t0) cc_final: 0.7013 (t0) REVERT: A 83 MET cc_start: 0.8094 (mtt) cc_final: 0.7870 (mtt) REVERT: A 110 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8630 (p) REVERT: A 111 ASP cc_start: 0.7672 (t0) cc_final: 0.6767 (t0) REVERT: A 114 ASP cc_start: 0.8359 (m-30) cc_final: 0.7947 (m-30) REVERT: A 130 ASN cc_start: 0.7690 (m110) cc_final: 0.7380 (m110) REVERT: A 131 ASN cc_start: 0.8013 (t0) cc_final: 0.7804 (t0) REVERT: A 195 ASP cc_start: 0.7334 (t70) cc_final: 0.6968 (t0) REVERT: B 165 THR cc_start: 0.8008 (t) cc_final: 0.7634 (m) REVERT: B 291 ASP cc_start: 0.7707 (m-30) cc_final: 0.7363 (m-30) outliers start: 22 outliers final: 14 residues processed: 394 average time/residue: 0.1421 time to fit residues: 85.8334 Evaluate side-chains 390 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 375 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 565 CYS Chi-restraints excluded: chain Q residue 583 ASN Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 144 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 174 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.093617 restraints weight = 28862.238| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.65 r_work: 0.2988 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18635 Z= 0.202 Angle : 0.571 9.828 25286 Z= 0.300 Chirality : 0.044 0.202 2831 Planarity : 0.004 0.057 3187 Dihedral : 6.656 62.207 2862 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.80 % Allowed : 9.69 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2219 helix: 1.24 (0.17), residues: 914 sheet: -1.47 (0.25), residues: 375 loop : -0.75 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.016 0.002 TYR R 421 PHE 0.018 0.002 PHE A 70 TRP 0.019 0.002 TRP Q 818 HIS 0.004 0.001 HIS R 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (18605) covalent geometry : angle 0.56001 / 0.30 (25212) SS BOND : bond 0.00249 / 0.18 ( 16) SS BOND : angle 2.33279 / 1.56 ( 32) hydrogen bonds : bond 0.05220 / 3.48 ( 868) hydrogen bonds : angle 4.77106 / 3.42 ( 2487) link_BETA1-4 : bond 0.00317 / 0.21 ( 4) link_BETA1-4 : angle 1.14468 / 0.77 ( 12) link_NAG-ASN : bond 0.00284 / 0.22 ( 10) link_NAG-ASN : angle 2.17522 / 1.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 384 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7470 (pp20) cc_final: 0.6817 (pp20) REVERT: R 52 LYS cc_start: 0.8200 (mttt) cc_final: 0.7796 (mtpt) REVERT: R 191 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7782 (mm-30) REVERT: R 636 LYS cc_start: 0.7775 (mtmt) cc_final: 0.7126 (mmtm) REVERT: R 756 LEU cc_start: 0.8287 (mt) cc_final: 0.7983 (mt) REVERT: A 43 ASN cc_start: 0.7790 (t0) cc_final: 0.6969 (t0) REVERT: A 82 HIS cc_start: 0.7345 (t70) cc_final: 0.6904 (t70) REVERT: A 110 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 111 ASP cc_start: 0.7732 (t0) cc_final: 0.6997 (t0) REVERT: A 114 ASP cc_start: 0.8394 (m-30) cc_final: 0.8068 (m-30) REVERT: A 195 ASP cc_start: 0.7395 (t70) cc_final: 0.7034 (t0) REVERT: A 238 MET cc_start: 0.8029 (ttm) cc_final: 0.7790 (ttt) REVERT: B 165 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7695 (m) REVERT: B 291 ASP cc_start: 0.7765 (m-30) cc_final: 0.7422 (m-30) outliers start: 35 outliers final: 22 residues processed: 399 average time/residue: 0.1353 time to fit residues: 83.2040 Evaluate side-chains 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 364 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 173 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 171 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094771 restraints weight = 28865.827| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.65 r_work: 0.2998 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18635 Z= 0.158 Angle : 0.540 9.403 25286 Z= 0.284 Chirality : 0.043 0.208 2831 Planarity : 0.004 0.052 3187 Dihedral : 6.305 58.078 2862 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 11.65 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2219 helix: 1.31 (0.17), residues: 918 sheet: -1.45 (0.25), residues: 370 loop : -0.68 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.014 0.001 TYR R 421 PHE 0.027 0.001 PHE A 74 TRP 0.017 0.001 TRP Q 818 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (18605) covalent geometry : angle 0.52937 / 0.28 (25212) SS BOND : bond 0.00169 / 0.12 ( 16) SS BOND : angle 2.18764 / 1.45 ( 32) hydrogen bonds : bond 0.04879 / 3.28 ( 868) hydrogen bonds : angle 4.64855 / 3.33 ( 2487) link_BETA1-4 : bond 0.00279 / 0.17 ( 4) link_BETA1-4 : angle 1.10659 / 0.76 ( 12) link_NAG-ASN : bond 0.00244 / 0.20 ( 10) link_NAG-ASN : angle 2.23341 / 1.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7438 (pp20) cc_final: 0.6779 (pp20) REVERT: Q 773 LEU cc_start: 0.8696 (tt) cc_final: 0.8486 (tp) REVERT: R 52 LYS cc_start: 0.8208 (mttt) cc_final: 0.7816 (mtpt) REVERT: R 191 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7762 (mm-30) REVERT: R 636 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7095 (mmtm) REVERT: R 756 LEU cc_start: 0.8345 (mt) cc_final: 0.8007 (mt) REVERT: A 43 ASN cc_start: 0.7821 (t0) cc_final: 0.6974 (t0) REVERT: A 82 HIS cc_start: 0.7279 (t70) cc_final: 0.6951 (t70) REVERT: A 110 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 111 ASP cc_start: 0.7795 (t0) cc_final: 0.7019 (t0) REVERT: A 114 ASP cc_start: 0.8362 (m-30) cc_final: 0.8060 (m-30) REVERT: A 131 ASN cc_start: 0.8100 (t0) cc_final: 0.7885 (t0) REVERT: A 195 ASP cc_start: 0.7378 (t70) cc_final: 0.7030 (t0) REVERT: B 165 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7760 (m) REVERT: B 291 ASP cc_start: 0.7761 (m-30) cc_final: 0.7454 (m-30) outliers start: 41 outliers final: 27 residues processed: 396 average time/residue: 0.1304 time to fit residues: 80.0749 Evaluate side-chains 393 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 364 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 733 PHE Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 11 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 163 optimal weight: 0.0980 chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094096 restraints weight = 28748.620| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.66 r_work: 0.2985 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18635 Z= 0.196 Angle : 0.562 8.834 25286 Z= 0.295 Chirality : 0.044 0.204 2831 Planarity : 0.004 0.050 3187 Dihedral : 6.235 57.042 2862 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.32 % Allowed : 12.84 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2219 helix: 1.30 (0.16), residues: 916 sheet: -1.53 (0.25), residues: 380 loop : -0.73 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 54 TYR 0.015 0.002 TYR R 421 PHE 0.015 0.002 PHE B 199 TRP 0.019 0.002 TRP Q 818 HIS 0.004 0.001 HIS R 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (18605) covalent geometry : angle 0.55015 / 0.29 (25212) SS BOND : bond 0.00210 / 0.14 ( 16) SS BOND : angle 2.44074 / 1.68 ( 32) hydrogen bonds : bond 0.05049 / 3.39 ( 868) hydrogen bonds : angle 4.68318 / 3.35 ( 2487) link_BETA1-4 : bond 0.00234 / 0.14 ( 4) link_BETA1-4 : angle 1.15676 / 0.79 ( 12) link_NAG-ASN : bond 0.00274 / 0.22 ( 10) link_NAG-ASN : angle 2.17769 / 1.04 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 773 LEU cc_start: 0.8709 (tt) cc_final: 0.8502 (tp) REVERT: R 52 LYS cc_start: 0.8254 (mttt) cc_final: 0.7844 (mtpt) REVERT: R 636 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7101 (mmtm) REVERT: R 756 LEU cc_start: 0.8384 (mt) cc_final: 0.8055 (mt) REVERT: A 43 ASN cc_start: 0.7870 (t0) cc_final: 0.6987 (t0) REVERT: A 82 HIS cc_start: 0.7264 (t70) cc_final: 0.7010 (t70) REVERT: A 111 ASP cc_start: 0.7793 (t0) cc_final: 0.7015 (t0) REVERT: A 114 ASP cc_start: 0.8365 (m-30) cc_final: 0.8061 (m-30) REVERT: A 131 ASN cc_start: 0.8098 (t0) cc_final: 0.7864 (t0) REVERT: A 195 ASP cc_start: 0.7420 (t70) cc_final: 0.7062 (t0) REVERT: B 291 ASP cc_start: 0.7802 (m-30) cc_final: 0.7445 (m-30) outliers start: 45 outliers final: 34 residues processed: 388 average time/residue: 0.1367 time to fit residues: 81.8951 Evaluate side-chains 392 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 358 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093056 restraints weight = 28670.636| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.64 r_work: 0.2975 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18635 Z= 0.231 Angle : 0.587 8.348 25286 Z= 0.307 Chirality : 0.045 0.205 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.304 58.027 2862 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 13.76 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2219 helix: 1.16 (0.16), residues: 922 sheet: -1.58 (0.25), residues: 380 loop : -0.78 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 54 TYR 0.016 0.002 TYR R 421 PHE 0.030 0.002 PHE A 74 TRP 0.019 0.002 TRP Q 818 HIS 0.005 0.001 HIS R 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (18605) covalent geometry : angle 0.57795 / 0.30 (25212) SS BOND : bond 0.00299 / 0.22 ( 16) SS BOND : angle 2.01864 / 1.27 ( 32) hydrogen bonds : bond 0.05221 / 3.49 ( 868) hydrogen bonds : angle 4.74556 / 3.39 ( 2487) link_BETA1-4 : bond 0.00194 / 0.11 ( 4) link_BETA1-4 : angle 1.21380 / 0.82 ( 12) link_NAG-ASN : bond 0.00307 / 0.25 ( 10) link_NAG-ASN : angle 2.23383 / 1.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 360 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7482 (pp20) cc_final: 0.6834 (pp20) REVERT: Q 773 LEU cc_start: 0.8717 (tt) cc_final: 0.8508 (tp) REVERT: R 52 LYS cc_start: 0.8249 (mttt) cc_final: 0.7811 (mtpt) REVERT: R 99 ASP cc_start: 0.7841 (t0) cc_final: 0.7619 (t70) REVERT: R 636 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7103 (mmtm) REVERT: R 756 LEU cc_start: 0.8404 (mt) cc_final: 0.8085 (mt) REVERT: A 43 ASN cc_start: 0.7846 (t0) cc_final: 0.6994 (t0) REVERT: A 82 HIS cc_start: 0.7279 (t70) cc_final: 0.6961 (t70) REVERT: A 111 ASP cc_start: 0.7808 (t0) cc_final: 0.6967 (t0) REVERT: A 114 ASP cc_start: 0.8383 (m-30) cc_final: 0.8048 (m-30) REVERT: A 119 GLN cc_start: 0.7306 (tp40) cc_final: 0.7042 (tp-100) REVERT: A 131 ASN cc_start: 0.8071 (t0) cc_final: 0.7805 (t0) REVERT: A 195 ASP cc_start: 0.7395 (t70) cc_final: 0.7057 (t0) REVERT: B 93 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8661 (mm) REVERT: B 258 ASP cc_start: 0.7846 (t0) cc_final: 0.7643 (t0) REVERT: B 291 ASP cc_start: 0.7832 (m-30) cc_final: 0.7459 (m-30) outliers start: 43 outliers final: 35 residues processed: 383 average time/residue: 0.1310 time to fit residues: 77.4348 Evaluate side-chains 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 352 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 134 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093258 restraints weight = 28928.649| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.62 r_work: 0.2978 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18635 Z= 0.213 Angle : 0.578 9.207 25286 Z= 0.301 Chirality : 0.044 0.206 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.247 56.785 2862 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 14.23 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2219 helix: 1.17 (0.16), residues: 926 sheet: -1.60 (0.25), residues: 380 loop : -0.79 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 185 TYR 0.015 0.002 TYR R 421 PHE 0.016 0.002 PHE A 70 TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS R 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (18605) covalent geometry : angle 0.56984 / 0.30 (25212) SS BOND : bond 0.00288 / 0.21 ( 16) SS BOND : angle 1.76280 / 1.10 ( 32) hydrogen bonds : bond 0.05109 / 3.42 ( 868) hydrogen bonds : angle 4.71954 / 3.37 ( 2487) link_BETA1-4 : bond 0.00203 / 0.12 ( 4) link_BETA1-4 : angle 1.20868 / 0.83 ( 12) link_NAG-ASN : bond 0.00298 / 0.24 ( 10) link_NAG-ASN : angle 2.21182 / 1.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 361 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7489 (pp20) cc_final: 0.6861 (pp20) REVERT: R 52 LYS cc_start: 0.8224 (mttt) cc_final: 0.7802 (mtpt) REVERT: R 636 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7111 (mmtm) REVERT: R 756 LEU cc_start: 0.8457 (mt) cc_final: 0.8145 (mt) REVERT: A 43 ASN cc_start: 0.7885 (t0) cc_final: 0.7132 (t0) REVERT: A 82 HIS cc_start: 0.7276 (t70) cc_final: 0.7051 (t70) REVERT: A 119 GLN cc_start: 0.7274 (tp40) cc_final: 0.7067 (tp-100) REVERT: A 120 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7428 (tp30) REVERT: A 131 ASN cc_start: 0.8073 (t0) cc_final: 0.7802 (t0) REVERT: A 195 ASP cc_start: 0.7379 (t70) cc_final: 0.7045 (t0) REVERT: B 59 TYR cc_start: 0.8427 (m-10) cc_final: 0.8099 (m-10) REVERT: B 291 ASP cc_start: 0.7812 (m-30) cc_final: 0.7506 (m-30) outliers start: 42 outliers final: 37 residues processed: 383 average time/residue: 0.1319 time to fit residues: 78.1555 Evaluate side-chains 391 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 354 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 583 ASN Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 486 VAL Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 135 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093137 restraints weight = 28971.181| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.65 r_work: 0.2977 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18635 Z= 0.209 Angle : 0.586 9.435 25286 Z= 0.305 Chirality : 0.045 0.241 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.221 56.254 2862 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.47 % Allowed : 14.33 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2219 helix: 1.21 (0.16), residues: 922 sheet: -1.57 (0.25), residues: 380 loop : -0.79 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 54 TYR 0.015 0.002 TYR R 421 PHE 0.033 0.002 PHE A 74 TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (18605) covalent geometry : angle 0.57851 / 0.30 (25212) SS BOND : bond 0.00302 / 0.22 ( 16) SS BOND : angle 1.64222 / 1.05 ( 32) hydrogen bonds : bond 0.05074 / 3.40 ( 868) hydrogen bonds : angle 4.72778 / 3.38 ( 2487) link_BETA1-4 : bond 0.00207 / 0.12 ( 4) link_BETA1-4 : angle 1.19670 / 0.81 ( 12) link_NAG-ASN : bond 0.00302 / 0.24 ( 10) link_NAG-ASN : angle 2.25751 / 1.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7495 (pp20) cc_final: 0.6882 (pp20) REVERT: R 52 LYS cc_start: 0.8219 (mttt) cc_final: 0.7788 (mtpt) REVERT: R 636 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7118 (mmtm) REVERT: R 756 LEU cc_start: 0.8456 (mt) cc_final: 0.8157 (mt) REVERT: A 43 ASN cc_start: 0.7857 (t0) cc_final: 0.7210 (t0) REVERT: A 82 HIS cc_start: 0.7344 (t70) cc_final: 0.7125 (t70) REVERT: A 111 ASP cc_start: 0.7712 (t0) cc_final: 0.6984 (t0) REVERT: A 114 ASP cc_start: 0.8155 (m-30) cc_final: 0.7895 (m-30) REVERT: A 120 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7442 (tp30) REVERT: A 131 ASN cc_start: 0.8083 (t0) cc_final: 0.7807 (t0) REVERT: A 195 ASP cc_start: 0.7395 (t70) cc_final: 0.7050 (t0) REVERT: A 242 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 59 TYR cc_start: 0.8421 (m-10) cc_final: 0.8074 (m-10) REVERT: B 291 ASP cc_start: 0.7813 (m-30) cc_final: 0.7492 (m-30) REVERT: B 340 ASN cc_start: 0.8142 (t0) cc_final: 0.7850 (t0) REVERT: G 51 LEU cc_start: 0.8530 (tp) cc_final: 0.8240 (mp) outliers start: 48 outliers final: 36 residues processed: 385 average time/residue: 0.1382 time to fit residues: 81.9282 Evaluate side-chains 391 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 486 VAL Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 0.2980 chunk 201 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093101 restraints weight = 28699.790| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.63 r_work: 0.2985 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18635 Z= 0.188 Angle : 0.581 9.221 25286 Z= 0.301 Chirality : 0.044 0.207 2831 Planarity : 0.004 0.050 3187 Dihedral : 6.152 56.316 2862 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 15.10 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2219 helix: 1.24 (0.16), residues: 923 sheet: -1.55 (0.25), residues: 380 loop : -0.77 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.023 0.002 TYR R 573 PHE 0.015 0.002 PHE A 70 TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (18605) covalent geometry : angle 0.57305 / 0.30 (25212) SS BOND : bond 0.00263 / 0.19 ( 16) SS BOND : angle 1.74373 / 1.12 ( 32) hydrogen bonds : bond 0.04944 / 3.31 ( 868) hydrogen bonds : angle 4.69441 / 3.36 ( 2487) link_BETA1-4 : bond 0.00207 / 0.12 ( 4) link_BETA1-4 : angle 1.17846 / 0.80 ( 12) link_NAG-ASN : bond 0.00295 / 0.24 ( 10) link_NAG-ASN : angle 2.19765 / 1.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7479 (pp20) cc_final: 0.6907 (pp20) REVERT: R 52 LYS cc_start: 0.8233 (mttt) cc_final: 0.7810 (mtpt) REVERT: R 481 GLU cc_start: 0.7485 (mp0) cc_final: 0.7247 (mp0) REVERT: R 636 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7104 (mmtm) REVERT: R 756 LEU cc_start: 0.8456 (mt) cc_final: 0.8162 (mt) REVERT: A 43 ASN cc_start: 0.7836 (t0) cc_final: 0.7175 (t0) REVERT: A 73 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (tppt) REVERT: A 82 HIS cc_start: 0.7362 (t70) cc_final: 0.7083 (t70) REVERT: A 111 ASP cc_start: 0.7671 (t0) cc_final: 0.6906 (t0) REVERT: A 114 ASP cc_start: 0.8164 (m-30) cc_final: 0.7896 (m-30) REVERT: A 120 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7441 (tp30) REVERT: A 131 ASN cc_start: 0.8105 (t0) cc_final: 0.7843 (t0) REVERT: A 195 ASP cc_start: 0.7394 (t70) cc_final: 0.7055 (t0) REVERT: A 242 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 59 TYR cc_start: 0.8390 (m-10) cc_final: 0.8036 (m-80) REVERT: B 291 ASP cc_start: 0.7789 (m-30) cc_final: 0.7572 (m-30) REVERT: B 340 ASN cc_start: 0.8064 (t0) cc_final: 0.7753 (t0) outliers start: 38 outliers final: 35 residues processed: 373 average time/residue: 0.1403 time to fit residues: 80.5452 Evaluate side-chains 387 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 351 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 486 VAL Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 42 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094305 restraints weight = 28832.725| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.64 r_work: 0.2992 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18635 Z= 0.164 Angle : 0.567 9.383 25286 Z= 0.294 Chirality : 0.044 0.245 2831 Planarity : 0.004 0.049 3187 Dihedral : 6.033 57.560 2862 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.96 % Allowed : 15.36 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2219 helix: 1.32 (0.16), residues: 923 sheet: -1.49 (0.25), residues: 380 loop : -0.75 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 54 TYR 0.019 0.001 TYR R 573 PHE 0.031 0.002 PHE A 74 TRP 0.017 0.001 TRP Q 818 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (18605) covalent geometry : angle 0.56007 / 0.29 (25212) SS BOND : bond 0.00258 / 0.18 ( 16) SS BOND : angle 1.56944 / 1.01 ( 32) hydrogen bonds : bond 0.04787 / 3.21 ( 868) hydrogen bonds : angle 4.62281 / 3.31 ( 2487) link_BETA1-4 : bond 0.00268 / 0.17 ( 4) link_BETA1-4 : angle 1.19903 / 0.83 ( 12) link_NAG-ASN : bond 0.00263 / 0.21 ( 10) link_NAG-ASN : angle 2.14091 / 1.04 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7480 (pp20) cc_final: 0.6885 (pp20) REVERT: Q 773 LEU cc_start: 0.8728 (tt) cc_final: 0.8511 (tp) REVERT: R 52 LYS cc_start: 0.8220 (mttt) cc_final: 0.7804 (mtpt) REVERT: R 636 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7102 (mmtm) REVERT: A 43 ASN cc_start: 0.7842 (t0) cc_final: 0.7216 (t0) REVERT: A 73 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8168 (tppt) REVERT: A 82 HIS cc_start: 0.7402 (t70) cc_final: 0.7095 (t70) REVERT: A 111 ASP cc_start: 0.7664 (t0) cc_final: 0.6864 (t0) REVERT: A 114 ASP cc_start: 0.8127 (m-30) cc_final: 0.7852 (m-30) REVERT: A 130 ASN cc_start: 0.7679 (m110) cc_final: 0.7332 (m110) REVERT: A 131 ASN cc_start: 0.8080 (t0) cc_final: 0.7799 (t0) REVERT: A 195 ASP cc_start: 0.7380 (t70) cc_final: 0.7166 (t0) REVERT: A 242 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 48 ARG cc_start: 0.6897 (mmm-85) cc_final: 0.6680 (mmm-85) REVERT: B 59 TYR cc_start: 0.8374 (m-10) cc_final: 0.7997 (m-80) REVERT: B 340 ASN cc_start: 0.8216 (t0) cc_final: 0.7849 (t0) outliers start: 38 outliers final: 33 residues processed: 377 average time/residue: 0.1366 time to fit residues: 79.1183 Evaluate side-chains 382 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 126 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 178 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093593 restraints weight = 28841.654| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.65 r_work: 0.2975 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18635 Z= 0.211 Angle : 0.601 10.394 25286 Z= 0.310 Chirality : 0.045 0.217 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.148 58.263 2862 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.01 % Allowed : 15.21 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2219 helix: 1.24 (0.16), residues: 925 sheet: -1.56 (0.25), residues: 380 loop : -0.82 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 54 TYR 0.019 0.002 TYR R 573 PHE 0.016 0.002 PHE A 70 TRP 0.019 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (18605) covalent geometry : angle 0.59340 / 0.31 (25212) SS BOND : bond 0.00299 / 0.21 ( 16) SS BOND : angle 1.68796 / 1.09 ( 32) hydrogen bonds : bond 0.05017 / 3.35 ( 868) hydrogen bonds : angle 4.67834 / 3.35 ( 2487) link_BETA1-4 : bond 0.00213 / 0.13 ( 4) link_BETA1-4 : angle 1.24916 / 0.88 ( 12) link_NAG-ASN : bond 0.00296 / 0.24 ( 10) link_NAG-ASN : angle 2.23183 / 1.07 ( 30) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4508.22 seconds wall clock time: 77 minutes 45.87 seconds (4665.87 seconds total)