Starting phenix.real_space_refine on Thu Sep 18 23:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axf_43966/09_2025/9axf_43966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axf_43966/09_2025/9axf_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_43966/09_2025/9axf_43966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axf_43966/09_2025/9axf_43966.map" model { file = "/net/cci-nas-00/data/ceres_data/9axf_43966/09_2025/9axf_43966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axf_43966/09_2025/9axf_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-2.0-5805/lib/python3.9/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, 287 Unusual residues: {' CA': 3, '9IG': 1, 'AV0': 1, 'CLR': 3, 'PO4': 1, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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, 205 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 5, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 4.91, 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 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: 0.90 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: 4.92 Time building geometry restraints manager: 2.34 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: 12.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.960 Find NCS groups from input model: 0.310 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 aren 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 covalent geometry : bond 0.00510 (21865) covalent geometry : angle 0.77928 (29710) SS BOND : bond 0.00297 ( 22) SS BOND : angle 1.54000 ( 44) hydrogen bonds : bond 0.14264 ( 952) hydrogen bonds : angle 5.78848 ( 2691) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 1.32130 ( 12) link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 1.81555 ( 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 : 0.795 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: 0.1773 time to fit residues: 112.6110 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3215 r_free = 0.3215 target = 0.101208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085342 restraints weight = 34531.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086855 restraints weight = 24383.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089025 restraints weight = 18404.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089192 restraints weight = 14629.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089360 restraints weight = 13468.347| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.0810 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= 0.180 Angle : 0.572 7.309 29802 Z= 0.303 Chirality : 0.044 0.211 3364 Planarity : 0.005 0.054 3690 Dihedral : 8.772 137.122 4110 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.29 % Allowed : 6.32 % Favored : 92.39 % 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 aren not related in a simple way. whole: 0.44 (0.16), residues: 2581 helix: 1.75 (0.17), residues: 884 sheet: 0.01 (0.22), residues: 558 loop : -0.69 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 54 TYR 0.015 0.002 TYR H 210 PHE 0.020 0.002 PHE A 74 TRP 0.017 0.002 TRP Q 818 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00427 (21865) covalent geometry : angle 0.56535 (29710) SS BOND : bond 0.00361 ( 22) SS BOND : angle 1.66927 ( 44) hydrogen bonds : bond 0.05846 ( 952) hydrogen bonds : angle 4.68459 ( 2691) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 1.26887 ( 12) link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 1.78528 ( 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 391 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 362 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 96 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7658 (mtp180) REVERT: Q 270 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 238 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8094 (ttp) REVERT: B 75 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7955 (mm-40) REVERT: B 270 ILE cc_start: 0.8340 (pt) cc_final: 0.8137 (pt) REVERT: H 230 THR cc_start: 0.8224 (p) cc_final: 0.8002 (p) outliers start: 29 outliers final: 21 residues processed: 372 average time/residue: 0.1729 time to fit residues: 96.0349 Evaluate side-chains 372 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 349 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 159 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 176 optimal weight: 0.0570 chunk 109 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086333 restraints weight = 34593.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088057 restraints weight = 24266.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.089876 restraints weight = 18078.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090079 restraints weight = 14761.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090494 restraints weight = 13672.961| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1044 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= 0.125 Angle : 0.505 6.664 29802 Z= 0.268 Chirality : 0.042 0.196 3364 Planarity : 0.004 0.050 3690 Dihedral : 7.884 106.476 4110 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 7.84 % Favored : 90.38 % 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 aren not related in a simple way. whole: 0.65 (0.17), residues: 2581 helix: 1.99 (0.17), residues: 883 sheet: 0.08 (0.22), residues: 557 loop : -0.61 (0.18), residues: 1141 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 covalent geometry : bond 0.00283 (21865) covalent geometry : angle 0.49939 (29710) SS BOND : bond 0.00261 ( 22) SS BOND : angle 1.33790 ( 44) hydrogen bonds : bond 0.05079 ( 952) hydrogen bonds : angle 4.45045 ( 2691) link_BETA1-4 : bond 0.00432 ( 4) link_BETA1-4 : angle 1.23192 ( 12) link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.60258 ( 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 403 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8516 (t0) cc_final: 0.8275 (t0) REVERT: R 707 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6840 (mt-10) REVERT: R 730 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5981 (mp) REVERT: Q 96 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7661 (mtp180) REVERT: Q 270 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7765 (t80) REVERT: Q 340 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7354 (mmt90) REVERT: Q 476 GLN cc_start: 0.7802 (mm110) cc_final: 0.7512 (mp10) REVERT: A 238 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8063 (ttp) REVERT: H 230 THR cc_start: 0.8234 (p) cc_final: 0.8006 (p) outliers start: 40 outliers final: 29 residues processed: 377 average time/residue: 0.1680 time to fit residues: 94.6153 Evaluate side-chains 376 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU 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 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 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain A residue 4 THR 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 63 SER 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: 1.9990 chunk 177 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 235 optimal weight: 0.0870 chunk 170 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.084103 restraints weight = 34701.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085580 restraints weight = 24725.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086875 restraints weight = 19057.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087345 restraints weight = 16114.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087982 restraints weight = 14738.857| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21903 Z= 0.214 Angle : 0.581 8.438 29802 Z= 0.305 Chirality : 0.045 0.190 3364 Planarity : 0.005 0.052 3690 Dihedral : 7.612 80.504 4110 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.40 % Allowed : 8.99 % Favored : 88.60 % 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 aren not related in a simple way. whole: 0.50 (0.16), residues: 2581 helix: 1.80 (0.17), residues: 896 sheet: -0.05 (0.22), residues: 561 loop : -0.63 (0.18), residues: 1124 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 0.021 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 covalent geometry : bond 0.00524 (21865) covalent geometry : angle 0.57424 (29710) SS BOND : bond 0.00404 ( 22) SS BOND : angle 1.60565 ( 44) hydrogen bonds : bond 0.05960 ( 952) hydrogen bonds : angle 4.55400 ( 2691) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.53592 ( 12) link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.92793 ( 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 417 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 453 LYS cc_start: 0.7862 (mttt) cc_final: 0.7585 (mtpp) REVERT: R 700 ASN cc_start: 0.8492 (t0) cc_final: 0.8249 (t0) REVERT: R 730 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6166 (mp) REVERT: Q 96 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7726 (mtp180) REVERT: Q 190 ASP cc_start: 0.7934 (m-30) cc_final: 0.7624 (m-30) REVERT: Q 270 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7837 (t80) REVERT: Q 340 ARG cc_start: 0.7661 (mtt-85) cc_final: 0.7418 (mmt90) REVERT: Q 476 GLN cc_start: 0.7791 (mm110) cc_final: 0.7524 (mp10) REVERT: Q 576 GLU cc_start: 0.7530 (pm20) cc_final: 0.7318 (pm20) REVERT: A 238 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8115 (ttp) REVERT: H 226 SER cc_start: 0.8562 (m) cc_final: 0.8307 (p) REVERT: H 230 THR cc_start: 0.8288 (p) cc_final: 0.8077 (p) outliers start: 54 outliers final: 44 residues processed: 383 average time/residue: 0.1507 time to fit residues: 86.2948 Evaluate side-chains 405 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 358 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 592 ASN 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 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: 0.7980 chunk 94 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 166 optimal weight: 0.0270 chunk 65 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 211 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 132 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.086102 restraints weight = 34300.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087165 restraints weight = 27421.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088126 restraints weight = 22905.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088596 restraints weight = 19565.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.088747 restraints weight = 18182.750| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21903 Z= 0.101 Angle : 0.474 6.375 29802 Z= 0.252 Chirality : 0.041 0.179 3364 Planarity : 0.004 0.048 3690 Dihedral : 6.669 57.243 4110 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 10.51 % Favored : 87.67 % 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 aren not related in a simple way. whole: 0.84 (0.17), residues: 2581 helix: 2.14 (0.17), residues: 886 sheet: 0.06 (0.22), residues: 563 loop : -0.42 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 25 TYR 0.014 0.001 TYR H 80 PHE 0.019 0.001 PHE A 74 TRP 0.015 0.001 TRP Q 818 HIS 0.004 0.001 HIS Q 41 Details of bonding type rmsd covalent geometry : bond 0.00214 (21865) covalent geometry : angle 0.46882 (29710) SS BOND : bond 0.00426 ( 22) SS BOND : angle 1.04876 ( 44) hydrogen bonds : bond 0.04478 ( 952) hydrogen bonds : angle 4.28740 ( 2691) link_BETA1-4 : bond 0.00352 ( 4) link_BETA1-4 : angle 1.11810 ( 12) link_NAG-ASN : bond 0.00311 ( 12) link_NAG-ASN : angle 1.57888 ( 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 420 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 454 LYS cc_start: 0.7740 (mttm) cc_final: 0.7371 (mtmm) REVERT: R 700 ASN cc_start: 0.8554 (t0) cc_final: 0.8307 (t0) REVERT: Q 96 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7664 (mtp180) REVERT: Q 190 ASP cc_start: 0.7682 (m-30) cc_final: 0.7435 (m-30) REVERT: Q 270 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7868 (t80) REVERT: Q 340 ARG cc_start: 0.7610 (mtt-85) cc_final: 0.7394 (mmt90) REVERT: Q 760 ILE cc_start: 0.8606 (mt) cc_final: 0.8377 (mt) REVERT: Q 794 SER cc_start: 0.8485 (m) cc_final: 0.8222 (p) REVERT: A 110 VAL cc_start: 0.8612 (t) cc_final: 0.8380 (p) REVERT: B 334 SER cc_start: 0.8421 (t) cc_final: 0.8204 (p) REVERT: N 60 TYR cc_start: 0.8173 (m-80) cc_final: 0.7918 (m-80) outliers start: 41 outliers final: 27 residues processed: 394 average time/residue: 0.1657 time to fit residues: 97.9856 Evaluate side-chains 390 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU 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 869 ILE 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 744 TYR Chi-restraints excluded: chain A residue 4 THR 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 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 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 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: 0.6980 chunk 183 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 137 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 65 optimal weight: 0.2980 chunk 186 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 512 ASN R 647 ASN R 724 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086041 restraints weight = 34272.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087022 restraints weight = 27851.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087954 restraints weight = 23105.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088373 restraints weight = 20153.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088520 restraints weight = 18509.295| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21903 Z= 0.112 Angle : 0.483 7.006 29802 Z= 0.256 Chirality : 0.041 0.186 3364 Planarity : 0.004 0.047 3690 Dihedral : 6.459 51.137 4110 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 10.69 % Favored : 87.31 % 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 aren not related in a simple way. whole: 0.85 (0.17), residues: 2581 helix: 2.14 (0.17), residues: 899 sheet: 0.08 (0.22), residues: 563 loop : -0.43 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 54 TYR 0.013 0.001 TYR H 210 PHE 0.019 0.001 PHE A 74 TRP 0.015 0.001 TRP Q 818 HIS 0.004 0.001 HIS Q 41 Details of bonding type rmsd covalent geometry : bond 0.00252 (21865) covalent geometry : angle 0.47672 (29710) SS BOND : bond 0.00242 ( 22) SS BOND : angle 1.40151 ( 44) hydrogen bonds : bond 0.04562 ( 952) hydrogen bonds : angle 4.23588 ( 2691) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.18893 ( 12) link_NAG-ASN : bond 0.00266 ( 12) link_NAG-ASN : angle 1.56572 ( 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 414 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: R 700 ASN cc_start: 0.8520 (t0) cc_final: 0.8273 (t0) REVERT: R 730 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5828 (mp) REVERT: R 776 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6881 (mp) REVERT: Q 96 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7697 (mtp180) REVERT: Q 190 ASP cc_start: 0.7688 (m-30) cc_final: 0.7432 (m-30) REVERT: Q 270 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7874 (t80) REVERT: Q 286 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7205 (mtp180) REVERT: Q 340 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7420 (mmt90) REVERT: Q 456 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: Q 794 SER cc_start: 0.8486 (m) cc_final: 0.8223 (p) REVERT: A 110 VAL cc_start: 0.8603 (t) cc_final: 0.8383 (p) REVERT: B 334 SER cc_start: 0.8364 (t) cc_final: 0.8153 (p) REVERT: N 60 TYR cc_start: 0.8168 (m-80) cc_final: 0.7922 (m-80) outliers start: 45 outliers final: 33 residues processed: 392 average time/residue: 0.1697 time to fit residues: 100.2712 Evaluate side-chains 402 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 364 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 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 437 CYS Chi-restraints excluded: chain Q residue 456 GLU 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 A residue 4 THR 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 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 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 N residue 63 SER Chi-restraints excluded: chain N residue 83 MET 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: 0.6980 chunk 226 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085228 restraints weight = 34336.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086379 restraints weight = 27756.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087554 restraints weight = 22516.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087891 restraints weight = 19479.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087959 restraints weight = 17797.611| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21903 Z= 0.138 Angle : 0.504 6.639 29802 Z= 0.267 Chirality : 0.042 0.196 3364 Planarity : 0.004 0.048 3690 Dihedral : 6.386 52.536 4110 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.32 % Allowed : 10.82 % Favored : 86.87 % 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 aren not related in a simple way. whole: 0.81 (0.17), residues: 2581 helix: 2.11 (0.17), residues: 899 sheet: 0.01 (0.22), residues: 563 loop : -0.44 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 54 TYR 0.013 0.001 TYR H 210 PHE 0.018 0.001 PHE A 74 TRP 0.016 0.001 TRP Q 818 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00323 (21865) covalent geometry : angle 0.49919 (29710) SS BOND : bond 0.00296 ( 22) SS BOND : angle 1.18549 ( 44) hydrogen bonds : bond 0.04922 ( 952) hydrogen bonds : angle 4.26446 ( 2691) link_BETA1-4 : bond 0.00294 ( 4) link_BETA1-4 : angle 1.29380 ( 12) link_NAG-ASN : bond 0.00185 ( 12) link_NAG-ASN : angle 1.61257 ( 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 427 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.740 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: 0.8017 (m-80) REVERT: R 512 ASN cc_start: 0.8611 (t0) cc_final: 0.8375 (t0) REVERT: R 700 ASN cc_start: 0.8506 (t0) cc_final: 0.8268 (t0) REVERT: R 730 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5942 (mp) REVERT: R 776 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6945 (mp) REVERT: Q 96 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7706 (mtp180) REVERT: Q 270 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7838 (t80) REVERT: Q 456 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: Q 794 SER cc_start: 0.8446 (m) cc_final: 0.8197 (p) REVERT: B 101 MET cc_start: 0.8189 (mtt) cc_final: 0.7920 (mtt) REVERT: B 334 SER cc_start: 0.8387 (t) cc_final: 0.8164 (p) REVERT: N 60 TYR cc_start: 0.8176 (m-80) cc_final: 0.7936 (m-80) outliers start: 52 outliers final: 40 residues processed: 398 average time/residue: 0.1734 time to fit residues: 103.9485 Evaluate side-chains 408 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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 776 LEU Chi-restraints excluded: chain R residue 865 SER 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 270 PHE 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 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 LYS 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 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 N residue 83 MET 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: 0.8980 chunk 159 optimal weight: 0.8980 chunk 194 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 230 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 524 ASN A 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085194 restraints weight = 34359.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.086590 restraints weight = 27833.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087296 restraints weight = 22136.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087847 restraints weight = 19678.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.088002 restraints weight = 18123.079| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1532 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= 0.140 Angle : 0.508 6.584 29802 Z= 0.269 Chirality : 0.042 0.201 3364 Planarity : 0.004 0.047 3690 Dihedral : 6.287 52.817 4110 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.40 % Allowed : 11.13 % 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 aren not related in a simple way. whole: 0.82 (0.17), residues: 2581 helix: 2.12 (0.17), residues: 895 sheet: 0.03 (0.22), residues: 567 loop : -0.43 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.013 0.001 TYR H 210 PHE 0.021 0.001 PHE A 74 TRP 0.016 0.001 TRP Q 818 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00330 (21865) covalent geometry : angle 0.50279 (29710) SS BOND : bond 0.00289 ( 22) SS BOND : angle 1.14952 ( 44) hydrogen bonds : bond 0.04930 ( 952) hydrogen bonds : angle 4.27146 ( 2691) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.29896 ( 12) link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 1.66561 ( 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 418 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 364 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: R 700 ASN cc_start: 0.8490 (t0) cc_final: 0.8271 (t0) REVERT: R 730 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5950 (mp) REVERT: R 776 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6963 (mp) REVERT: Q 96 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7711 (mtp180) REVERT: Q 270 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7835 (t80) REVERT: Q 456 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: Q 794 SER cc_start: 0.8503 (m) cc_final: 0.8252 (p) REVERT: B 101 MET cc_start: 0.8209 (mtt) cc_final: 0.7943 (mtt) REVERT: B 334 SER cc_start: 0.8393 (t) cc_final: 0.8157 (p) REVERT: N 60 TYR cc_start: 0.8179 (m-80) cc_final: 0.7960 (m-80) outliers start: 54 outliers final: 45 residues processed: 389 average time/residue: 0.1551 time to fit residues: 91.7632 Evaluate side-chains 412 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 776 LEU Chi-restraints excluded: chain R residue 865 SER 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 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 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 LYS 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 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 89 THR 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 63 SER Chi-restraints excluded: chain N residue 83 MET 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 216 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 524 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.085488 restraints weight = 34388.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.087223 restraints weight = 24405.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.088869 restraints weight = 18366.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.089082 restraints weight = 15445.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089164 restraints weight = 14318.267| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21903 Z= 0.158 Angle : 0.530 10.950 29802 Z= 0.279 Chirality : 0.042 0.207 3364 Planarity : 0.004 0.048 3690 Dihedral : 6.313 55.037 4110 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 11.18 % 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 aren not related in a simple way. whole: 0.79 (0.17), residues: 2581 helix: 2.08 (0.17), residues: 895 sheet: 0.03 (0.22), residues: 566 loop : -0.45 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.014 0.001 TYR N 95 PHE 0.024 0.001 PHE A 74 TRP 0.016 0.002 TRP Q 818 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00379 (21865) covalent geometry : angle 0.52453 (29710) SS BOND : bond 0.00321 ( 22) SS BOND : angle 1.19924 ( 44) hydrogen bonds : bond 0.05150 ( 952) hydrogen bonds : angle 4.30750 ( 2691) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.33681 ( 12) link_NAG-ASN : bond 0.00193 ( 12) link_NAG-ASN : angle 1.72266 ( 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 417 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: R 307 MET cc_start: 0.7469 (mtp) cc_final: 0.7261 (mtm) REVERT: R 512 ASN cc_start: 0.8601 (t0) cc_final: 0.8286 (t0) REVERT: R 700 ASN cc_start: 0.8518 (t0) cc_final: 0.8244 (t0) REVERT: R 730 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5961 (mp) REVERT: R 776 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6969 (mp) REVERT: Q 96 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7717 (mtp180) REVERT: Q 190 ASP cc_start: 0.7918 (m-30) cc_final: 0.7591 (m-30) REVERT: Q 270 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7848 (t80) REVERT: Q 456 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: Q 794 SER cc_start: 0.8504 (m) cc_final: 0.8244 (p) REVERT: B 334 SER cc_start: 0.8479 (t) cc_final: 0.8217 (p) REVERT: N 60 TYR cc_start: 0.8174 (m-80) cc_final: 0.7927 (m-80) outliers start: 58 outliers final: 46 residues processed: 387 average time/residue: 0.1612 time to fit residues: 94.8398 Evaluate side-chains 405 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 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 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 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 LYS 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 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 89 THR 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 63 SER Chi-restraints excluded: chain N residue 83 MET 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: 2.9990 chunk 195 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 255 optimal weight: 0.0040 chunk 76 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 524 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.084836 restraints weight = 34408.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086029 restraints weight = 27635.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086845 restraints weight = 22620.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.087308 restraints weight = 19932.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087459 restraints weight = 18360.895| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21903 Z= 0.159 Angle : 0.539 9.753 29802 Z= 0.283 Chirality : 0.042 0.210 3364 Planarity : 0.004 0.048 3690 Dihedral : 6.303 59.725 4110 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.36 % Allowed : 11.71 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.17), residues: 2581 helix: 2.05 (0.17), residues: 895 sheet: 0.04 (0.22), residues: 566 loop : -0.47 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.015 0.001 TYR N 95 PHE 0.022 0.001 PHE A 74 TRP 0.016 0.002 TRP Q 818 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00380 (21865) covalent geometry : angle 0.53341 (29710) SS BOND : bond 0.00320 ( 22) SS BOND : angle 1.19668 ( 44) hydrogen bonds : bond 0.05180 ( 952) hydrogen bonds : angle 4.31806 ( 2691) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.32986 ( 12) link_NAG-ASN : bond 0.00202 ( 12) link_NAG-ASN : angle 1.74163 ( 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 414 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 361 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: R 512 ASN cc_start: 0.8613 (t0) cc_final: 0.8277 (t0) REVERT: R 700 ASN cc_start: 0.8478 (t0) cc_final: 0.8226 (t0) REVERT: R 730 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5985 (mp) REVERT: R 776 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7003 (mp) REVERT: Q 96 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7709 (mtp180) REVERT: Q 190 ASP cc_start: 0.7909 (m-30) cc_final: 0.7575 (m-30) REVERT: Q 270 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7863 (t80) REVERT: Q 456 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: Q 794 SER cc_start: 0.8533 (m) cc_final: 0.8279 (p) REVERT: B 334 SER cc_start: 0.8486 (t) cc_final: 0.8209 (p) REVERT: N 60 TYR cc_start: 0.8191 (m-80) cc_final: 0.7951 (m-80) outliers start: 53 outliers final: 44 residues processed: 386 average time/residue: 0.1653 time to fit residues: 97.0328 Evaluate side-chains 402 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 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 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 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE 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 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 89 THR 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 63 SER Chi-restraints excluded: chain N residue 83 MET 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: 1.9990 chunk 254 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 201 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN R 855 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 429 HIS Q 495 HIS Q 524 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.084902 restraints weight = 34665.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.086324 restraints weight = 24793.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087437 restraints weight = 19178.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.087989 restraints weight = 16497.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.088315 restraints weight = 15081.425| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21903 Z= 0.161 Angle : 0.540 11.417 29802 Z= 0.284 Chirality : 0.043 0.208 3364 Planarity : 0.004 0.048 3690 Dihedral : 6.279 54.491 4110 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.18 % Allowed : 11.98 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.17), residues: 2581 helix: 2.04 (0.17), residues: 895 sheet: -0.00 (0.22), residues: 566 loop : -0.47 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 54 TYR 0.015 0.001 TYR N 95 PHE 0.023 0.001 PHE A 74 TRP 0.016 0.002 TRP Q 818 HIS 0.010 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00387 (21865) covalent geometry : angle 0.53475 (29710) SS BOND : bond 0.00328 ( 22) SS BOND : angle 1.21147 ( 44) hydrogen bonds : bond 0.05227 ( 952) hydrogen bonds : angle 4.33986 ( 2691) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 1.32904 ( 12) link_NAG-ASN : bond 0.00191 ( 12) link_NAG-ASN : angle 1.76477 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.79 seconds wall clock time: 66 minutes 53.20 seconds (4013.20 seconds total)