Starting phenix.real_space_refine on Sat Jul 4 14:01:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.map" model { file = "/net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axf_43966/07_2026/9axf_43966.cif" } resolution = 3.5 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= 0.043 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 7 9.91 5 P 2 5.49 5 S 123 5.16 5 Cl 2 4.86 5 C 13769 2.51 5 N 3464 2.21 5 O 3975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 21342 Number of models: 1 Model: "" Number of chains: 15 Chain: "R" Number of atoms: 6632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6632 Classifications: {'peptide': 832} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 798} Chain breaks: 1 Chain: "Q" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6293 Classifications: {'peptide': 791} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 759} Chain breaks: 2 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1879 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} 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: "H" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} 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: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 4, 'TCR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 284 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'9IG': 1, 'AV0': 1, 'CLR': 3, 'PO4': 1, 'Y01': 3} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 4, 'TCR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 201 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'9IG': 1, 'CLR': 5, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 4 Time building chain proxies: 4.87, per 1000 atoms: 0.23 Number of scatterers: 21342 At special positions: 0 Unit cell: (108.876, 132.508, 245.604, 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 7 19.99 Cl 2 17.00 S 123 16.00 P 2 15.00 O 3975 8.00 N 3464 7.00 C 13769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 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 546 " - pdb=" SG CYS R 565 " 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 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.04 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 437 " - pdb=" SG CYS Q 449 " 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 H 42 " - pdb=" SG CYS H 116 " distance=2.04 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 249 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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 R 488 " " NAG D 1 " - " ASN R 541 " " NAG E 1 " - " ASN Q 488 " " NAG F 1 " - " ASN Q 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG Q1004 " - " ASN Q 594 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " " NAG R1004 " - " ASN R 594 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 31 sheets defined 39.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 116 removed outlier: 3.533A pdb=" N ALA R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 removed outlier: 3.549A pdb=" N ILE R 120 " --> pdb=" O GLN R 117 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP R 121 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER R 122 " --> pdb=" O LYS R 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 122' Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.838A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.516A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.740A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix 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 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: 3.849A 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 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.532A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 666 Processing helix chain 'R' and resid 673 through 707 removed outlier: 4.828A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.643A pdb=" N VAL R 689 " --> pdb=" O GLY R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 716 through 746 removed outlier: 3.603A pdb=" N PHE R 725 " --> pdb=" O LEU R 721 " (cutoff:3.500A) Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.761A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 804 through 814 removed outlier: 3.961A pdb=" N THR R 808 " --> pdb=" O ALA R 804 " (cutoff:3.500A) Processing helix chain 'R' and resid 816 through 821 removed outlier: 3.567A pdb=" N PHE R 821 " --> pdb=" O VAL R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 821 through 827 Processing helix chain 'R' and resid 830 through 862 removed outlier: 3.984A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE R 853 " --> pdb=" O LEU R 849 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 Processing helix chain 'R' and resid 868 through 882 Processing helix chain 'Q' and resid 21 through 25 removed outlier: 4.015A pdb=" N ARG Q 25 " --> pdb=" O PRO Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 84 Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.560A pdb=" N ALA Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 121 Processing helix chain 'Q' and resid 146 through 159 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.828A 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: 3.675A 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 357 Processing helix chain 'Q' and resid 400 through 404 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 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 645 Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.712A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 669 removed outlier: 3.949A pdb=" N ILE Q 669 " --> pdb=" O LEU Q 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 666 through 669' Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.916A 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 723 through 746 removed outlier: 3.842A pdb=" N MET Q 734 " --> pdb=" O LEU Q 730 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.719A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER Q 794 " --> pdb=" O PHE Q 790 " (cutoff:3.500A) Processing helix chain 'Q' and resid 798 through 828 removed outlier: 6.062A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 832 through 853 removed outlier: 3.612A pdb=" N VAL Q 836 " --> pdb=" O PHE Q 832 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Q 845 " --> pdb=" O ILE Q 841 " (cutoff:3.500A) Processing helix chain 'Q' and resid 853 through 862 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.661A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.644A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.244A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.700A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.555A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.504A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 82 through 85 removed outlier: 3.636A pdb=" N LYS H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 85' Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 240 through 244 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.775A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.022A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.028A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 318 through 322 removed outlier: 6.843A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.529A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 550 through 551 Processing sheet with id=AA7, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AA9, first strand: chain 'R' and resid 602 through 604 removed outlier: 3.607A pdb=" N ILE R 763 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.468A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 8.068A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL Q 266 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 469 through 470 Processing sheet with id=AB4, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AB5, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'Q' and resid 602 through 604 removed outlier: 3.662A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 71 through 75 removed outlier: 3.818A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.337A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.520A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.855A 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: 7.029A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.455A 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 234 removed outlier: 6.527A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.635A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AC7, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.085A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR H 70 " --> pdb=" O MET H 54 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP H 56 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.085A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE H 130 " --> pdb=" O ARG H 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.545A pdb=" N ALA H 231 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 214 through 215 removed outlier: 6.437A pdb=" N TRP H 196 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 210 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU H 194 " --> pdb=" O TYR H 210 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR H 258 " --> pdb=" O GLN H 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 214 through 215 removed outlier: 6.437A pdb=" N TRP H 196 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 210 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU H 194 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.370A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6686 1.34 - 1.46: 5204 1.46 - 1.58: 9814 1.58 - 1.70: 2 1.70 - 1.82: 159 Bond restraints: 21865 Sorted by residual: bond pdb=" CAI Y01 R1013 " pdb=" CAK Y01 R1013 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAI Y01 R1014 " pdb=" CAK Y01 R1014 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CAI Y01 Q1012 " pdb=" CAK Y01 Q1012 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAI Y01 R1012 " pdb=" CAK Y01 R1012 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O4 PO4 Q1006 " pdb=" P PO4 Q1006 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.70e+00 ... (remaining 21860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 29127 2.37 - 4.73: 491 4.73 - 7.10: 61 7.10 - 9.46: 19 9.46 - 11.83: 12 Bond angle restraints: 29710 Sorted by residual: angle pdb=" CAM Y01 Q1012 " pdb=" CAY Y01 Q1012 " pdb=" OAW Y01 Q1012 " ideal model delta sigma weight residual 111.19 123.02 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ILE Q 305 " pdb=" CA ILE Q 305 " pdb=" C ILE Q 305 " ideal model delta sigma weight residual 111.90 108.71 3.19 8.10e-01 1.52e+00 1.55e+01 angle pdb=" OAG Y01 R1013 " pdb=" CAY Y01 R1013 " pdb=" OAW Y01 R1013 " ideal model delta sigma weight residual 123.38 111.76 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" OAG Y01 R1014 " pdb=" CAY Y01 R1014 " pdb=" OAW Y01 R1014 " ideal model delta sigma weight residual 123.38 111.78 11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" OAG Y01 Q1012 " pdb=" CAY Y01 Q1012 " pdb=" OAW Y01 Q1012 " ideal model delta sigma weight residual 123.38 111.85 11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 29705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 13486 32.72 - 65.43: 283 65.43 - 98.15: 21 98.15 - 130.86: 1 130.86 - 163.58: 2 Dihedral angle restraints: 13793 sinusoidal: 6230 harmonic: 7563 Sorted by residual: 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 93.00 179.09 -86.09 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS Q 60 " pdb=" SG CYS Q 60 " pdb=" SG CYS Q 101 " pdb=" CB CYS Q 101 " ideal model delta sinusoidal sigma weight residual -86.00 -21.45 -64.55 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS Q 585 " pdb=" SG CYS Q 585 " pdb=" SG CYS Q 598 " pdb=" CB CYS Q 598 " ideal model delta sinusoidal sigma weight residual -86.00 -137.64 51.64 1 1.00e+01 1.00e-02 3.64e+01 ... (remaining 13790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2988 0.079 - 0.159: 315 0.159 - 0.238: 23 0.238 - 0.317: 27 0.317 - 0.397: 11 Chirality restraints: 3364 Sorted by residual: chirality pdb=" C17 CLR Q1013 " pdb=" C13 CLR Q1013 " pdb=" C16 CLR Q1013 " pdb=" C20 CLR Q1013 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C17 CLR R1015 " pdb=" C13 CLR R1015 " pdb=" C16 CLR R1015 " pdb=" C20 CLR R1015 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C17 CLR Q1017 " pdb=" C13 CLR Q1017 " pdb=" C16 CLR Q1017 " pdb=" C20 CLR Q1017 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 3361 not shown) Planarity restraints: 3702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 88 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO Q 89 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO Q 89 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Q 89 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 172 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 173 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 425 " 0.015 2.00e-02 2.50e+03 1.78e-02 6.32e+00 pdb=" CG TYR Q 425 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 425 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 425 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 425 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 425 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR Q 425 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 425 " -0.004 2.00e-02 2.50e+03 ... (remaining 3699 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 612 2.71 - 3.26: 20715 3.26 - 3.80: 33396 3.80 - 4.35: 44273 4.35 - 4.90: 74668 Nonbonded interactions: 173664 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.162 3.120 nonbonded pdb=" O ILE Q 741 " pdb=" OG1 THR Q 745 " model vdw 2.210 3.040 nonbonded pdb=" OG SER N 17 " pdb=" OD1 ASN N 84 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU B 215 " pdb=" NH2 ARG B 219 " model vdw 2.254 3.120 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.261 3.120 ... (remaining 173659 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 20 through 1009 or resid 1012 or resid 1015 through 1017)) \ selection = (chain 'R' and (resid 20 through 700 or resid 723 through 863 or resid 1001 thro \ ugh 1009 or resid 1012 or resid 1015 through 1017)) } 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 group one per residue 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: 9.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.590 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.088 21903 Z= 0.248 Angle : 0.783 11.829 29802 Z= 0.383 Chirality : 0.057 0.397 3364 Planarity : 0.005 0.068 3690 Dihedral : 13.153 163.577 8849 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2581 helix: 1.30 (0.17), residues: 897 sheet: -0.15 (0.22), residues: 560 loop : -0.72 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 286 TYR 0.042 0.002 TYR Q 425 PHE 0.020 0.001 PHE B 234 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 (21865) covalent geometry : angle 0.77928 / 0.38 (29710) SS BOND : bond 0.00297 / 0.16 ( 22) SS BOND : angle 1.54000 / 1.04 ( 44) hydrogen bonds : bond 0.14264 / 9.55 ( 952) hydrogen bonds : angle 5.78848 / 4.12 ( 2691) link_BETA1-4 : bond 0.00373 / 0.19 ( 4) link_BETA1-4 : angle 1.32130 / 0.74 ( 12) link_NAG-ASN : bond 0.00301 / 0.15 ( 12) link_NAG-ASN : angle 1.81555 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 679 LEU cc_start: 0.8119 (tp) cc_final: 0.7899 (tp) REVERT: R 865 SER cc_start: 0.8938 (m) cc_final: 0.8526 (t) REVERT: Q 31 ASP cc_start: 0.7743 (m-30) cc_final: 0.7510 (m-30) REVERT: Q 96 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7810 (mtp-110) REVERT: Q 354 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7256 (mp0) REVERT: Q 476 GLN cc_start: 0.7896 (mm110) cc_final: 0.7627 (mp10) REVERT: Q 760 ILE cc_start: 0.8569 (mt) cc_final: 0.8318 (mt) REVERT: A 110 VAL cc_start: 0.8477 (t) cc_final: 0.8203 (p) REVERT: A 242 GLU cc_start: 0.7477 (tp30) cc_final: 0.7013 (tp30) REVERT: B 76 ASP cc_start: 0.7488 (p0) cc_final: 0.7150 (p0) REVERT: B 270 ILE cc_start: 0.8419 (pt) cc_final: 0.8182 (pt) REVERT: H 230 THR cc_start: 0.8161 (p) cc_final: 0.7948 (p) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1664 time to fit residues: 106.4188 Evaluate side-chains 360 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 260 GLN ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.085184 restraints weight = 34554.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.086733 restraints weight = 24455.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088919 restraints weight = 18439.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089084 restraints weight = 14598.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.089287 restraints weight = 13516.897| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21903 Z= 0.176 Angle : 0.568 7.303 29802 Z= 0.301 Chirality : 0.044 0.218 3364 Planarity : 0.005 0.054 3690 Dihedral : 8.723 135.819 4110 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.34 % Allowed : 6.32 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2581 helix: 1.75 (0.17), residues: 884 sheet: 0.01 (0.22), residues: 558 loop : -0.68 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 117 TYR 0.015 0.002 TYR H 210 PHE 0.020 0.002 PHE A 74 TRP 0.018 0.002 TRP Q 818 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (21865) covalent geometry : angle 0.56123 / 0.30 (29710) SS BOND : bond 0.00408 / 0.25 ( 22) SS BOND : angle 1.63612 / 1.09 ( 44) hydrogen bonds : bond 0.05874 / 3.94 ( 952) hydrogen bonds : angle 4.67312 / 3.36 ( 2691) link_BETA1-4 : bond 0.00351 / 0.18 ( 4) link_BETA1-4 : angle 1.26624 / 0.71 ( 12) link_NAG-ASN : bond 0.00273 / 0.13 ( 12) link_NAG-ASN : angle 1.77168 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8525 (t0) cc_final: 0.8243 (t0) REVERT: Q 96 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7648 (mtp180) REVERT: Q 270 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7702 (t80) REVERT: A 238 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: B 75 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7966 (mm-40) REVERT: B 301 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7789 (mttm) REVERT: H 230 THR cc_start: 0.8235 (p) cc_final: 0.8015 (p) outliers start: 30 outliers final: 22 residues processed: 370 average time/residue: 0.1724 time to fit residues: 95.4626 Evaluate side-chains 371 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 347 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 170 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 250 optimal weight: 0.0670 chunk 239 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 429 HIS A 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085995 restraints weight = 34630.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087661 restraints weight = 24506.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089749 restraints weight = 18287.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.089955 restraints weight = 14423.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089996 restraints weight = 13307.101| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21903 Z= 0.140 Angle : 0.517 7.055 29802 Z= 0.275 Chirality : 0.042 0.170 3364 Planarity : 0.004 0.050 3690 Dihedral : 7.842 102.387 4110 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.65 % Allowed : 8.10 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2581 helix: 1.93 (0.17), residues: 889 sheet: 0.06 (0.22), residues: 559 loop : -0.63 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 25 TYR 0.014 0.001 TYR H 210 PHE 0.020 0.001 PHE A 74 TRP 0.016 0.001 TRP Q 818 HIS 0.004 0.001 HIS Q 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21865) covalent geometry : angle 0.51082 / 0.27 (29710) SS BOND : bond 0.00408 / 0.25 ( 22) SS BOND : angle 1.42722 / 0.95 ( 44) hydrogen bonds : bond 0.05238 / 3.52 ( 952) hydrogen bonds : angle 4.46708 / 3.22 ( 2691) link_BETA1-4 : bond 0.00221 / 0.11 ( 4) link_BETA1-4 : angle 1.25755 / 0.70 ( 12) link_NAG-ASN : bond 0.00220 / 0.11 ( 12) link_NAG-ASN : angle 1.65250 / 0.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 365 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8532 (t0) cc_final: 0.8240 (t0) REVERT: R 730 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5984 (mp) REVERT: Q 96 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7667 (mtp180) REVERT: Q 270 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7782 (t80) REVERT: Q 286 ARG cc_start: 0.7628 (mtp180) cc_final: 0.7420 (mtp180) REVERT: Q 340 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.7360 (mmt90) REVERT: Q 476 GLN cc_start: 0.7805 (mm110) cc_final: 0.7519 (mp10) REVERT: Q 576 GLU cc_start: 0.7519 (pm20) cc_final: 0.7293 (pm20) REVERT: A 238 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8074 (ttp) REVERT: H 230 THR cc_start: 0.8250 (p) cc_final: 0.8020 (p) outliers start: 37 outliers final: 27 residues processed: 378 average time/residue: 0.1589 time to fit residues: 90.6474 Evaluate side-chains 389 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 143 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 724 GLN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 493 ASN Q 495 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.083819 restraints weight = 34767.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085678 restraints weight = 24661.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.086988 restraints weight = 18401.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.087266 restraints weight = 15739.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087513 restraints weight = 14602.667| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21903 Z= 0.212 Angle : 0.579 8.330 29802 Z= 0.304 Chirality : 0.044 0.180 3364 Planarity : 0.005 0.052 3690 Dihedral : 7.545 78.429 4110 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.40 % Allowed : 9.44 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.50 (0.16), residues: 2581 helix: 1.79 (0.17), residues: 896 sheet: -0.04 (0.22), residues: 565 loop : -0.64 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 25 TYR 0.015 0.002 TYR H 210 PHE 0.022 0.002 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.005 0.001 HIS Q 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (21865) covalent geometry : angle 0.57158 / 0.30 (29710) SS BOND : bond 0.00434 / 0.25 ( 22) SS BOND : angle 1.57585 / 1.05 ( 44) hydrogen bonds : bond 0.05961 / 4.01 ( 952) hydrogen bonds : angle 4.55910 / 3.27 ( 2691) link_BETA1-4 : bond 0.00296 / 0.15 ( 4) link_BETA1-4 : angle 1.52903 / 0.84 ( 12) link_NAG-ASN : bond 0.00199 / 0.09 ( 12) link_NAG-ASN : angle 1.91440 / 1.10 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 372 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 307 MET cc_start: 0.7566 (mtp) cc_final: 0.7360 (mtm) REVERT: R 453 LYS cc_start: 0.7854 (mttt) cc_final: 0.7585 (mtpp) REVERT: R 730 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6173 (mp) REVERT: Q 80 GLU cc_start: 0.7717 (tt0) cc_final: 0.7508 (tt0) REVERT: Q 96 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7724 (mtp180) REVERT: Q 190 ASP cc_start: 0.7931 (m-30) cc_final: 0.7631 (m-30) REVERT: Q 270 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7851 (t80) REVERT: Q 340 ARG cc_start: 0.7650 (mtt-85) cc_final: 0.7408 (mmt90) REVERT: Q 476 GLN cc_start: 0.7775 (mm110) cc_final: 0.7520 (mp10) REVERT: Q 576 GLU cc_start: 0.7623 (pm20) cc_final: 0.7354 (pm20) REVERT: A 238 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: H 226 SER cc_start: 0.8578 (m) cc_final: 0.8347 (p) REVERT: H 230 THR cc_start: 0.8292 (p) cc_final: 0.8079 (p) outliers start: 54 outliers final: 44 residues processed: 394 average time/residue: 0.1577 time to fit residues: 94.0607 Evaluate side-chains 414 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 228 GLU Chi-restraints excluded: chain Q residue 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 166 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 512 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.084882 restraints weight = 34483.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086579 restraints weight = 24352.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088486 restraints weight = 18239.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088710 restraints weight = 14742.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088784 restraints weight = 13627.158| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21903 Z= 0.154 Angle : 0.528 6.958 29802 Z= 0.279 Chirality : 0.042 0.186 3364 Planarity : 0.004 0.049 3690 Dihedral : 7.025 65.775 4110 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 9.97 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2581 helix: 1.93 (0.17), residues: 890 sheet: -0.06 (0.22), residues: 563 loop : -0.55 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 233 TYR 0.014 0.001 TYR H 210 PHE 0.021 0.001 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS H 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (21865) covalent geometry : angle 0.52148 / 0.28 (29710) SS BOND : bond 0.00334 / 0.18 ( 22) SS BOND : angle 1.36116 / 0.90 ( 44) hydrogen bonds : bond 0.05337 / 3.60 ( 952) hydrogen bonds : angle 4.44605 / 3.19 ( 2691) link_BETA1-4 : bond 0.00305 / 0.16 ( 4) link_BETA1-4 : angle 1.36865 / 0.76 ( 12) link_NAG-ASN : bond 0.00215 / 0.10 ( 12) link_NAG-ASN : angle 1.76461 / 1.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 373 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: R 307 MET cc_start: 0.7523 (mtp) cc_final: 0.7297 (mtm) REVERT: R 700 ASN cc_start: 0.8494 (t0) cc_final: 0.8264 (t0) REVERT: R 730 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6076 (mp) REVERT: Q 96 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7710 (mtp180) REVERT: Q 270 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7857 (t80) REVERT: Q 340 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7420 (mmt90) REVERT: Q 524 ASN cc_start: 0.7751 (m-40) cc_final: 0.7535 (m-40) REVERT: Q 576 GLU cc_start: 0.7655 (pm20) cc_final: 0.7394 (pm20) REVERT: A 238 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8075 (ttp) REVERT: H 226 SER cc_start: 0.8575 (m) cc_final: 0.8375 (p) REVERT: H 230 THR cc_start: 0.8294 (p) cc_final: 0.8065 (p) outliers start: 58 outliers final: 47 residues processed: 398 average time/residue: 0.1697 time to fit residues: 102.6262 Evaluate side-chains 414 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 0 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084454 restraints weight = 34501.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086354 restraints weight = 25212.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087391 restraints weight = 18683.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087754 restraints weight = 16344.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.088020 restraints weight = 15246.872| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21903 Z= 0.177 Angle : 0.546 7.521 29802 Z= 0.288 Chirality : 0.043 0.190 3364 Planarity : 0.004 0.050 3690 Dihedral : 6.879 59.859 4110 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.89 % Allowed : 10.42 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2581 helix: 1.88 (0.17), residues: 895 sheet: -0.11 (0.22), residues: 563 loop : -0.53 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 54 TYR 0.017 0.002 TYR N 95 PHE 0.019 0.002 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (21865) covalent geometry : angle 0.53933 / 0.29 (29710) SS BOND : bond 0.00341 / 0.19 ( 22) SS BOND : angle 1.42104 / 0.93 ( 44) hydrogen bonds : bond 0.05542 / 3.74 ( 952) hydrogen bonds : angle 4.45496 / 3.19 ( 2691) link_BETA1-4 : bond 0.00326 / 0.17 ( 4) link_BETA1-4 : angle 1.44608 / 0.80 ( 12) link_NAG-ASN : bond 0.00190 / 0.09 ( 12) link_NAG-ASN : angle 1.82867 / 1.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 367 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: R 307 MET cc_start: 0.7524 (mtp) cc_final: 0.7273 (mtm) REVERT: R 512 ASN cc_start: 0.8638 (t0) cc_final: 0.8286 (t0) REVERT: R 700 ASN cc_start: 0.8497 (t0) cc_final: 0.8264 (t0) REVERT: R 730 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6124 (mp) REVERT: R 776 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7008 (mp) REVERT: Q 80 GLU cc_start: 0.7665 (tt0) cc_final: 0.7457 (tt0) REVERT: Q 96 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7722 (mtp180) REVERT: Q 190 ASP cc_start: 0.7912 (m-30) cc_final: 0.7593 (m-30) REVERT: Q 270 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7888 (t80) REVERT: Q 340 ARG cc_start: 0.7663 (mtt-85) cc_final: 0.7444 (mmt90) REVERT: Q 524 ASN cc_start: 0.7761 (m-40) cc_final: 0.7542 (m-40) REVERT: Q 576 GLU cc_start: 0.7710 (pm20) cc_final: 0.7418 (pm20) REVERT: A 238 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8084 (ttp) REVERT: B 101 MET cc_start: 0.8200 (mtt) cc_final: 0.7982 (mtt) REVERT: H 226 SER cc_start: 0.8583 (m) cc_final: 0.8369 (p) REVERT: H 230 THR cc_start: 0.8304 (p) cc_final: 0.8096 (p) outliers start: 65 outliers final: 50 residues processed: 396 average time/residue: 0.1580 time to fit residues: 94.6911 Evaluate side-chains 415 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.084311 restraints weight = 34533.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085768 restraints weight = 24623.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086915 restraints weight = 19080.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.087440 restraints weight = 16334.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.087583 restraints weight = 14965.143| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21903 Z= 0.184 Angle : 0.551 7.532 29802 Z= 0.291 Chirality : 0.043 0.195 3364 Planarity : 0.004 0.052 3690 Dihedral : 6.765 57.109 4110 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 10.37 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2581 helix: 1.91 (0.17), residues: 890 sheet: -0.11 (0.22), residues: 567 loop : -0.54 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.016 0.002 TYR N 95 PHE 0.021 0.002 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (21865) covalent geometry : angle 0.54423 / 0.29 (29710) SS BOND : bond 0.00348 / 0.19 ( 22) SS BOND : angle 1.43962 / 0.96 ( 44) hydrogen bonds : bond 0.05575 / 3.76 ( 952) hydrogen bonds : angle 4.46549 / 3.20 ( 2691) link_BETA1-4 : bond 0.00303 / 0.16 ( 4) link_BETA1-4 : angle 1.45196 / 0.80 ( 12) link_NAG-ASN : bond 0.00197 / 0.09 ( 12) link_NAG-ASN : angle 1.85404 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 361 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: R 307 MET cc_start: 0.7462 (mtp) cc_final: 0.7244 (mtm) REVERT: R 512 ASN cc_start: 0.8617 (t0) cc_final: 0.8287 (t0) REVERT: R 700 ASN cc_start: 0.8482 (t0) cc_final: 0.8247 (t0) REVERT: R 730 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6075 (mp) REVERT: R 776 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7017 (mp) REVERT: Q 80 GLU cc_start: 0.7665 (tt0) cc_final: 0.7452 (tt0) REVERT: Q 96 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7718 (mtp180) REVERT: Q 270 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7842 (t80) REVERT: Q 456 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: Q 524 ASN cc_start: 0.7759 (m-40) cc_final: 0.7541 (m-40) REVERT: A 238 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8079 (ttp) REVERT: H 226 SER cc_start: 0.8590 (m) cc_final: 0.8371 (p) REVERT: H 230 THR cc_start: 0.8302 (p) cc_final: 0.8094 (p) outliers start: 71 outliers final: 56 residues processed: 395 average time/residue: 0.1665 time to fit residues: 100.3116 Evaluate side-chains 421 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 654 LEU Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 101 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 194 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.084224 restraints weight = 34404.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085445 restraints weight = 27638.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.086060 restraints weight = 22361.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086654 restraints weight = 20225.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086834 restraints weight = 18547.758| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21903 Z= 0.137 Angle : 0.517 8.506 29802 Z= 0.273 Chirality : 0.042 0.197 3364 Planarity : 0.004 0.049 3690 Dihedral : 6.480 54.523 4110 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.80 % Allowed : 10.95 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.71 (0.17), residues: 2581 helix: 2.04 (0.17), residues: 889 sheet: -0.07 (0.22), residues: 566 loop : -0.47 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.014 0.001 TYR H 210 PHE 0.019 0.001 PHE A 74 TRP 0.017 0.001 TRP Q 818 HIS 0.004 0.001 HIS H 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21865) covalent geometry : angle 0.51182 / 0.27 (29710) SS BOND : bond 0.00275 / 0.15 ( 22) SS BOND : angle 1.24935 / 0.83 ( 44) hydrogen bonds : bond 0.05068 / 3.41 ( 952) hydrogen bonds : angle 4.35601 / 3.13 ( 2691) link_BETA1-4 : bond 0.00290 / 0.15 ( 4) link_BETA1-4 : angle 1.29556 / 0.72 ( 12) link_NAG-ASN : bond 0.00253 / 0.12 ( 12) link_NAG-ASN : angle 1.73156 / 0.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 374 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: R 512 ASN cc_start: 0.8599 (t0) cc_final: 0.8287 (t0) REVERT: R 700 ASN cc_start: 0.8495 (t0) cc_final: 0.8251 (t0) REVERT: R 707 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6829 (mt-10) REVERT: R 730 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.6020 (mp) REVERT: R 776 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6993 (mp) REVERT: Q 96 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7696 (mtp180) REVERT: Q 270 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7831 (t80) REVERT: Q 456 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: A 238 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8052 (ttp) REVERT: B 101 MET cc_start: 0.8178 (mtt) cc_final: 0.7975 (mtt) REVERT: B 334 SER cc_start: 0.8482 (t) cc_final: 0.8216 (p) REVERT: H 230 THR cc_start: 0.8294 (p) cc_final: 0.8053 (p) outliers start: 63 outliers final: 50 residues processed: 406 average time/residue: 0.1462 time to fit residues: 91.0857 Evaluate side-chains 427 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 654 LEU Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.084301 restraints weight = 34502.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085817 restraints weight = 24697.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.087330 restraints weight = 19108.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087652 restraints weight = 15760.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.087905 restraints weight = 14498.215| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21903 Z= 0.193 Angle : 0.563 8.017 29802 Z= 0.296 Chirality : 0.044 0.205 3364 Planarity : 0.004 0.051 3690 Dihedral : 6.591 54.737 4110 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.80 % Allowed : 11.58 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2581 helix: 1.90 (0.17), residues: 895 sheet: -0.12 (0.22), residues: 564 loop : -0.55 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 54 TYR 0.014 0.002 TYR H 210 PHE 0.023 0.002 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (21865) covalent geometry : angle 0.55613 / 0.29 (29710) SS BOND : bond 0.00391 / 0.21 ( 22) SS BOND : angle 1.66354 / 1.07 ( 44) hydrogen bonds : bond 0.05577 / 3.76 ( 952) hydrogen bonds : angle 4.42616 / 3.17 ( 2691) link_BETA1-4 : bond 0.00310 / 0.16 ( 4) link_BETA1-4 : angle 1.42633 / 0.79 ( 12) link_NAG-ASN : bond 0.00202 / 0.09 ( 12) link_NAG-ASN : angle 1.83567 / 1.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 364 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: R 512 ASN cc_start: 0.8603 (t0) cc_final: 0.8287 (t0) REVERT: R 700 ASN cc_start: 0.8489 (t0) cc_final: 0.8256 (t0) REVERT: R 730 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6139 (mp) REVERT: R 776 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7025 (mp) REVERT: Q 80 GLU cc_start: 0.7655 (tt0) cc_final: 0.7438 (tt0) REVERT: Q 96 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7718 (mtp180) REVERT: Q 270 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7847 (t80) REVERT: Q 456 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: Q 524 ASN cc_start: 0.7637 (t0) cc_final: 0.7245 (t0) REVERT: A 238 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8095 (ttp) REVERT: H 230 THR cc_start: 0.8308 (p) cc_final: 0.8106 (p) outliers start: 63 outliers final: 52 residues processed: 397 average time/residue: 0.1562 time to fit residues: 94.6005 Evaluate side-chains 420 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 362 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 255 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 194 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.084779 restraints weight = 34579.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085956 restraints weight = 24596.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086713 restraints weight = 20868.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087486 restraints weight = 17852.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087648 restraints weight = 16838.309| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21903 Z= 0.166 Angle : 0.543 8.443 29802 Z= 0.286 Chirality : 0.043 0.206 3364 Planarity : 0.004 0.050 3690 Dihedral : 6.473 53.828 4110 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.63 % Allowed : 11.62 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.63 (0.17), residues: 2581 helix: 1.96 (0.17), residues: 889 sheet: -0.10 (0.22), residues: 564 loop : -0.51 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.014 0.001 TYR H 210 PHE 0.024 0.001 PHE A 228 TRP 0.017 0.002 TRP Q 818 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21865) covalent geometry : angle 0.53633 / 0.28 (29710) SS BOND : bond 0.00328 / 0.17 ( 22) SS BOND : angle 1.41022 / 0.92 ( 44) hydrogen bonds : bond 0.05342 / 3.60 ( 952) hydrogen bonds : angle 4.39362 / 3.15 ( 2691) link_BETA1-4 : bond 0.00304 / 0.16 ( 4) link_BETA1-4 : angle 1.35830 / 0.75 ( 12) link_NAG-ASN : bond 0.00200 / 0.09 ( 12) link_NAG-ASN : angle 1.80388 / 1.02 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 365 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: R 512 ASN cc_start: 0.8591 (t0) cc_final: 0.8282 (t0) REVERT: R 700 ASN cc_start: 0.8497 (t0) cc_final: 0.8263 (t0) REVERT: R 730 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6108 (mp) REVERT: R 776 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7007 (mp) REVERT: Q 80 GLU cc_start: 0.7650 (tt0) cc_final: 0.7431 (tt0) REVERT: Q 96 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7712 (mtp180) REVERT: Q 190 ASP cc_start: 0.8049 (m-30) cc_final: 0.7789 (m-30) REVERT: Q 270 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7851 (t80) REVERT: Q 456 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: Q 524 ASN cc_start: 0.7598 (t0) cc_final: 0.7201 (t0) REVERT: A 238 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8087 (ttp) REVERT: H 230 THR cc_start: 0.8306 (p) cc_final: 0.8070 (p) outliers start: 59 outliers final: 50 residues processed: 395 average time/residue: 0.1542 time to fit residues: 92.8708 Evaluate side-chains 418 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 208 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084390 restraints weight = 34690.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.086155 restraints weight = 24498.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087686 restraints weight = 18356.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087940 restraints weight = 15500.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.088117 restraints weight = 14294.542| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21903 Z= 0.173 Angle : 0.555 9.595 29802 Z= 0.292 Chirality : 0.043 0.210 3364 Planarity : 0.004 0.051 3690 Dihedral : 6.472 54.510 4110 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.94 % Allowed : 11.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2581 helix: 1.91 (0.17), residues: 895 sheet: -0.11 (0.22), residues: 564 loop : -0.53 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.014 0.002 TYR H 210 PHE 0.025 0.001 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS H 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (21865) covalent geometry : angle 0.54846 / 0.29 (29710) SS BOND : bond 0.00346 / 0.18 ( 22) SS BOND : angle 1.36945 / 0.91 ( 44) hydrogen bonds : bond 0.05433 / 3.66 ( 952) hydrogen bonds : angle 4.40550 / 3.16 ( 2691) link_BETA1-4 : bond 0.00297 / 0.15 ( 4) link_BETA1-4 : angle 1.37014 / 0.76 ( 12) link_NAG-ASN : bond 0.00195 / 0.09 ( 12) link_NAG-ASN : angle 1.84030 / 1.04 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.53 seconds wall clock time: 65 minutes 25.86 seconds (3925.86 seconds total)