Starting phenix.real_space_refine on Wed Jun 18 14:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axf_43966/06_2025/9axf_43966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axf_43966/06_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_43966/06_2025/9axf_43966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axf_43966/06_2025/9axf_43966.map" model { file = "/net/cci-nas-00/data/ceres_data/9axf_43966/06_2025/9axf_43966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axf_43966/06_2025/9axf_43966.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.18, per 1000 atoms: 0.66 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: 5.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 31 sheets defined 39.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 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: 7.92 Time building geometry restraints manager: 6.72 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 863 or resid 1001 through 1005 or resid 1006 th \ rough 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 1005 or resid 1006 through 1009 or resid 1012 or resid 1015 through 1017)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.090 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: 0.920 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 51.290 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.260 ------------------------------------------------------------------------------- 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 : 5.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE B 234 TYR 0.042 0.002 TYR Q 425 ARG 0.010 0.001 ARG Q 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 1.81555 ( 36) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 1.32130 ( 12) hydrogen bonds : bond 0.14264 ( 952) hydrogen bonds : angle 5.78848 ( 2691) SS BOND : bond 0.00297 ( 22) SS BOND : angle 1.54000 ( 44) covalent geometry : bond 0.00510 (21865) covalent geometry : angle 0.77928 (29710) *********************** 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 : 2.265 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: 0.3647 time to fit residues: 232.3359 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 : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.0470 chunk 194 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 201 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0170 chunk 149 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 260 GLN 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 = 0.3239 r_free = 0.3239 target = 0.102621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.086868 restraints weight = 34383.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088503 restraints weight = 24171.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090465 restraints weight = 18169.204| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21903 Z= 0.125 Angle : 0.527 6.947 29802 Z= 0.280 Chirality : 0.042 0.193 3364 Planarity : 0.004 0.052 3690 Dihedral : 8.584 135.886 4110 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 6.06 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2581 helix: 1.90 (0.17), residues: 882 sheet: 0.04 (0.22), residues: 558 loop : -0.63 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.004 0.001 HIS H 55 PHE 0.019 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.005 0.000 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 1.68268 ( 36) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 1.08862 ( 12) hydrogen bonds : bond 0.05168 ( 952) hydrogen bonds : angle 4.57576 ( 2691) SS BOND : bond 0.00338 ( 22) SS BOND : angle 1.40955 ( 44) covalent geometry : bond 0.00276 (21865) covalent geometry : angle 0.52097 (29710) *********************** 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 403 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8543 (t0) cc_final: 0.8242 (t0) REVERT: Q 96 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7758 (mtp180) REVERT: Q 270 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7677 (t80) REVERT: Q 760 ILE cc_start: 0.8634 (mt) cc_final: 0.8394 (mt) REVERT: A 110 VAL cc_start: 0.8544 (t) cc_final: 0.8302 (p) REVERT: A 147 ASP cc_start: 0.7544 (p0) cc_final: 0.7313 (p0) REVERT: A 148 LEU cc_start: 0.8867 (mt) cc_final: 0.8642 (mp) REVERT: B 75 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7903 (mm-40) REVERT: H 230 THR cc_start: 0.8217 (p) cc_final: 0.8005 (p) outliers start: 28 outliers final: 22 residues processed: 385 average time/residue: 0.3676 time to fit residues: 211.3596 Evaluate side-chains 379 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 356 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 799 GLU 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 744 TYR Chi-restraints excluded: chain Q residue 800 ASN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 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 16 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 24 GLN Q 429 HIS Q 493 ASN Q 495 HIS A 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.083364 restraints weight = 34470.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085017 restraints weight = 24499.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087019 restraints weight = 18382.627| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 21903 Z= 0.259 Angle : 0.633 8.721 29802 Z= 0.331 Chirality : 0.046 0.202 3364 Planarity : 0.005 0.053 3690 Dihedral : 8.263 106.262 4110 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.09 % Allowed : 7.93 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2581 helix: 1.69 (0.17), residues: 888 sheet: -0.01 (0.22), residues: 553 loop : -0.72 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 818 HIS 0.007 0.001 HIS Q 495 PHE 0.021 0.002 PHE A 74 TYR 0.016 0.002 TYR B 105 ARG 0.007 0.001 ARG Q 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 12) link_NAG-ASN : angle 1.97412 ( 36) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 1.69055 ( 12) hydrogen bonds : bond 0.06544 ( 952) hydrogen bonds : angle 4.70843 ( 2691) SS BOND : bond 0.00467 ( 22) SS BOND : angle 1.90573 ( 44) covalent geometry : bond 0.00639 (21865) covalent geometry : angle 0.62540 (29710) *********************** 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 417 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 730 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6178 (mp) REVERT: Q 270 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7859 (t80) REVERT: Q 286 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7431 (mtp180) REVERT: Q 340 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7403 (mmt90) REVERT: Q 576 GLU cc_start: 0.7560 (pm20) cc_final: 0.7336 (pm20) REVERT: A 185 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7211 (mtm-85) REVERT: H 226 SER cc_start: 0.8555 (m) cc_final: 0.8281 (p) outliers start: 47 outliers final: 36 residues processed: 384 average time/residue: 0.3576 time to fit residues: 206.0569 Evaluate side-chains 396 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 358 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 865 SER 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 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 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 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 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 246 optimal weight: 0.0570 chunk 111 optimal weight: 0.8980 chunk 219 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.084853 restraints weight = 34691.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086552 restraints weight = 24664.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088464 restraints weight = 18405.652| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21903 Z= 0.159 Angle : 0.536 7.195 29802 Z= 0.284 Chirality : 0.043 0.176 3364 Planarity : 0.004 0.049 3690 Dihedral : 7.473 77.673 4110 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.83 % Allowed : 10.02 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2581 helix: 1.85 (0.17), residues: 890 sheet: -0.05 (0.22), residues: 567 loop : -0.62 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.005 0.001 HIS A 209 PHE 0.021 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.005 0.000 ARG Q 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.79557 ( 36) link_BETA1-4 : bond 0.00297 ( 4) link_BETA1-4 : angle 1.35013 ( 12) hydrogen bonds : bond 0.05455 ( 952) hydrogen bonds : angle 4.52013 ( 2691) SS BOND : bond 0.00325 ( 22) SS BOND : angle 1.46083 ( 44) covalent geometry : bond 0.00378 (21865) covalent geometry : angle 0.52923 (29710) *********************** 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 403 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 307 MET cc_start: 0.7598 (mtp) cc_final: 0.7300 (mtm) REVERT: R 700 ASN cc_start: 0.8489 (t0) cc_final: 0.8253 (t0) REVERT: Q 270 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7840 (t80) REVERT: Q 286 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7426 (mtp180) REVERT: Q 340 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7412 (mmt90) REVERT: Q 576 GLU cc_start: 0.7635 (pm20) cc_final: 0.7366 (pm20) REVERT: H 226 SER cc_start: 0.8571 (m) cc_final: 0.8331 (p) outliers start: 41 outliers final: 36 residues processed: 380 average time/residue: 0.3592 time to fit residues: 205.6201 Evaluate side-chains 389 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 352 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 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 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR 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 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 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 161 THR Chi-restraints excluded: chain H residue 254 GLU 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 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 855 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.083914 restraints weight = 34517.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.085481 restraints weight = 24338.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.087199 restraints weight = 18815.115| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21903 Z= 0.219 Angle : 0.586 8.434 29802 Z= 0.308 Chirality : 0.044 0.182 3364 Planarity : 0.005 0.053 3690 Dihedral : 7.341 70.226 4110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.76 % Allowed : 10.11 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2581 helix: 1.72 (0.17), residues: 896 sheet: -0.11 (0.22), residues: 559 loop : -0.67 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.002 PHE A 74 TYR 0.018 0.002 TYR N 95 ARG 0.006 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.93992 ( 36) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 1.57242 ( 12) hydrogen bonds : bond 0.06006 ( 952) hydrogen bonds : angle 4.58466 ( 2691) SS BOND : bond 0.00405 ( 22) SS BOND : angle 1.61990 ( 44) covalent geometry : bond 0.00533 (21865) covalent geometry : angle 0.57912 (29710) *********************** 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 423 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: R 307 MET cc_start: 0.7600 (mtp) cc_final: 0.7360 (mtm) REVERT: R 453 LYS cc_start: 0.7873 (mttt) cc_final: 0.7603 (mtpp) REVERT: R 700 ASN cc_start: 0.8489 (t0) cc_final: 0.8252 (t0) REVERT: R 730 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6180 (mp) REVERT: Q 270 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7881 (t80) REVERT: Q 332 GLU cc_start: 0.7063 (mp0) cc_final: 0.6852 (mp0) REVERT: Q 340 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7453 (mmt90) REVERT: Q 576 GLU cc_start: 0.7692 (pm20) cc_final: 0.7415 (pm20) REVERT: H 226 SER cc_start: 0.8591 (m) cc_final: 0.8347 (p) outliers start: 62 outliers final: 52 residues processed: 388 average time/residue: 0.3821 time to fit residues: 223.3678 Evaluate side-chains 409 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 354 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 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 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 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 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 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 219 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.085212 restraints weight = 34448.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086675 restraints weight = 24466.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087736 restraints weight = 19062.479| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1414 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= 0.144 Angle : 0.520 6.562 29802 Z= 0.276 Chirality : 0.042 0.186 3364 Planarity : 0.004 0.050 3690 Dihedral : 6.860 59.004 4110 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 10.69 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2581 helix: 1.94 (0.17), residues: 889 sheet: -0.06 (0.22), residues: 566 loop : -0.56 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS Q 41 PHE 0.020 0.001 PHE A 74 TYR 0.014 0.001 TYR N 95 ARG 0.007 0.000 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.77167 ( 36) link_BETA1-4 : bond 0.00309 ( 4) link_BETA1-4 : angle 1.33206 ( 12) hydrogen bonds : bond 0.05215 ( 952) hydrogen bonds : angle 4.44290 ( 2691) SS BOND : bond 0.00323 ( 22) SS BOND : angle 1.33328 ( 44) covalent geometry : bond 0.00339 (21865) covalent geometry : angle 0.51355 (29710) *********************** 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 423 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: R 307 MET cc_start: 0.7526 (mtp) cc_final: 0.7319 (mtm) REVERT: R 454 LYS cc_start: 0.7822 (mttm) cc_final: 0.7451 (mtmm) REVERT: R 512 ASN cc_start: 0.8614 (t0) cc_final: 0.8293 (t0) REVERT: R 700 ASN cc_start: 0.8505 (t0) cc_final: 0.8263 (t0) REVERT: R 730 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.6082 (mp) REVERT: R 776 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6969 (mp) REVERT: Q 190 ASP cc_start: 0.7873 (m-30) cc_final: 0.7557 (m-30) REVERT: Q 270 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7879 (t80) REVERT: Q 340 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7515 (mmt90) REVERT: H 226 SER cc_start: 0.8575 (m) cc_final: 0.8345 (p) REVERT: N 60 TYR cc_start: 0.8169 (m-80) cc_final: 0.7960 (m-80) outliers start: 58 outliers final: 46 residues processed: 393 average time/residue: 0.4072 time to fit residues: 242.5481 Evaluate side-chains 410 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.084320 restraints weight = 34296.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085810 restraints weight = 24372.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086800 restraints weight = 18849.766| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21903 Z= 0.192 Angle : 0.561 7.813 29802 Z= 0.296 Chirality : 0.043 0.190 3364 Planarity : 0.004 0.052 3690 Dihedral : 6.859 59.604 4110 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.89 % Allowed : 11.18 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2581 helix: 1.82 (0.17), residues: 896 sheet: -0.09 (0.22), residues: 564 loop : -0.63 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.002 PHE A 74 TYR 0.014 0.002 TYR H 210 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 12) link_NAG-ASN : angle 1.87051 ( 36) link_BETA1-4 : bond 0.00313 ( 4) link_BETA1-4 : angle 1.47759 ( 12) hydrogen bonds : bond 0.05665 ( 952) hydrogen bonds : angle 4.48452 ( 2691) SS BOND : bond 0.00365 ( 22) SS BOND : angle 1.50618 ( 44) covalent geometry : bond 0.00467 (21865) covalent geometry : angle 0.55393 (29710) *********************** 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 419 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 354 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: R 512 ASN cc_start: 0.8627 (t0) cc_final: 0.8291 (t0) REVERT: R 700 ASN cc_start: 0.8496 (t0) cc_final: 0.8254 (t0) REVERT: R 730 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6112 (mp) REVERT: R 776 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7011 (mp) REVERT: Q 270 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7857 (t80) REVERT: Q 340 ARG cc_start: 0.7729 (mtt-85) cc_final: 0.7524 (mmt90) REVERT: Q 456 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: H 226 SER cc_start: 0.8599 (m) cc_final: 0.8363 (p) outliers start: 65 outliers final: 53 residues processed: 385 average time/residue: 0.3540 time to fit residues: 205.7817 Evaluate side-chains 408 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 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 R residue 869 ILE Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 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 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.100117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.083992 restraints weight = 34739.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.085530 restraints weight = 24572.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.086520 restraints weight = 18974.921| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21903 Z= 0.203 Angle : 0.575 8.352 29802 Z= 0.303 Chirality : 0.044 0.197 3364 Planarity : 0.004 0.054 3690 Dihedral : 6.822 59.588 4110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.98 % Allowed : 11.09 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2581 helix: 1.78 (0.17), residues: 896 sheet: -0.13 (0.22), residues: 560 loop : -0.63 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.006 0.001 HIS A 82 PHE 0.022 0.002 PHE A 74 TYR 0.015 0.002 TYR H 210 ARG 0.007 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 1.92224 ( 36) link_BETA1-4 : bond 0.00318 ( 4) link_BETA1-4 : angle 1.49308 ( 12) hydrogen bonds : bond 0.05747 ( 952) hydrogen bonds : angle 4.50654 ( 2691) SS BOND : bond 0.00377 ( 22) SS BOND : angle 1.53155 ( 44) covalent geometry : bond 0.00494 (21865) covalent geometry : angle 0.56839 (29710) *********************** 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 422 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 355 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: R 512 ASN cc_start: 0.8612 (t0) cc_final: 0.8294 (t0) REVERT: R 700 ASN cc_start: 0.8479 (t0) cc_final: 0.8230 (t0) REVERT: R 730 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6147 (mp) REVERT: R 776 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7023 (mp) REVERT: Q 270 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7844 (t80) REVERT: Q 340 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7545 (mmt90) REVERT: Q 456 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: H 226 SER cc_start: 0.8593 (m) cc_final: 0.8338 (p) outliers start: 67 outliers final: 56 residues processed: 388 average time/residue: 0.4732 time to fit residues: 284.9374 Evaluate side-chains 412 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 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 R residue 869 ILE Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 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 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 199 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 134 optimal weight: 0.0970 chunk 180 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.101213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.085180 restraints weight = 34216.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086691 restraints weight = 24363.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087624 restraints weight = 18992.859| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1566 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= 0.136 Angle : 0.523 8.352 29802 Z= 0.276 Chirality : 0.042 0.198 3364 Planarity : 0.004 0.052 3690 Dihedral : 6.504 55.366 4110 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.58 % Allowed : 11.75 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2581 helix: 1.99 (0.17), residues: 889 sheet: -0.07 (0.22), residues: 566 loop : -0.50 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS Q 41 PHE 0.022 0.001 PHE A 74 TYR 0.019 0.001 TYR R 435 ARG 0.006 0.000 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 12) link_NAG-ASN : angle 1.73137 ( 36) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.29028 ( 12) hydrogen bonds : bond 0.05061 ( 952) hydrogen bonds : angle 4.37582 ( 2691) SS BOND : bond 0.00284 ( 22) SS BOND : angle 1.27751 ( 44) covalent geometry : bond 0.00319 (21865) covalent geometry : angle 0.51743 (29710) *********************** 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 419 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 361 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: R 512 ASN cc_start: 0.8600 (t0) cc_final: 0.8286 (t0) REVERT: R 700 ASN cc_start: 0.8503 (t0) cc_final: 0.8245 (t0) REVERT: R 730 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6045 (mp) REVERT: R 776 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6976 (mp) REVERT: Q 270 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7864 (t80) REVERT: Q 456 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: B 334 SER cc_start: 0.8505 (t) cc_final: 0.8243 (p) outliers start: 58 outliers final: 48 residues processed: 388 average time/residue: 0.3604 time to fit residues: 212.8321 Evaluate side-chains 411 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 358 time to evaluate : 2.335 ------------------------------------------------------------------------------- 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 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 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 25 ARG 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 478 THR Chi-restraints excluded: chain Q residue 497 SER 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 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 98 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 135 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 239 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.099577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.083414 restraints weight = 34640.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.084911 restraints weight = 24710.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085876 restraints weight = 19188.872| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21903 Z= 0.235 Angle : 0.608 8.547 29802 Z= 0.318 Chirality : 0.045 0.205 3364 Planarity : 0.005 0.055 3690 Dihedral : 6.805 59.646 4110 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.63 % Allowed : 11.93 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2581 helix: 1.75 (0.17), residues: 896 sheet: -0.14 (0.22), residues: 562 loop : -0.65 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 PHE 0.026 0.002 PHE A 74 TYR 0.022 0.002 TYR N 60 ARG 0.008 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.97245 ( 36) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 1.54942 ( 12) hydrogen bonds : bond 0.06038 ( 952) hydrogen bonds : angle 4.53107 ( 2691) SS BOND : bond 0.00419 ( 22) SS BOND : angle 1.61766 ( 44) covalent geometry : bond 0.00576 (21865) covalent geometry : angle 0.60138 (29710) ********************** 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 412 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 353 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: R 307 MET cc_start: 0.7528 (mtp) cc_final: 0.7296 (mtm) REVERT: R 512 ASN cc_start: 0.8611 (t0) cc_final: 0.8297 (t0) REVERT: R 700 ASN cc_start: 0.8448 (t0) cc_final: 0.8203 (t0) REVERT: R 730 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6213 (mp) REVERT: R 776 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7050 (mp) REVERT: Q 270 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7857 (t80) REVERT: Q 456 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6412 (mp0) outliers start: 59 outliers final: 51 residues processed: 380 average time/residue: 0.3518 time to fit residues: 203.0547 Evaluate side-chains 404 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 456 GLU Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER 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 848 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 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 117 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 187 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 159 optimal weight: 0.0770 chunk 74 optimal weight: 0.3980 chunk 226 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 Q 524 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.085135 restraints weight = 34352.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086598 restraints weight = 24877.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087750 restraints weight = 19386.008| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1623 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 : 0.536 8.653 29802 Z= 0.283 Chirality : 0.042 0.205 3364 Planarity : 0.004 0.052 3690 Dihedral : 6.477 55.058 4110 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.54 % Allowed : 12.24 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2581 helix: 1.96 (0.17), residues: 889 sheet: -0.09 (0.22), residues: 566 loop : -0.53 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.006 0.001 HIS A 82 PHE 0.026 0.001 PHE Q 788 TYR 0.020 0.001 TYR R 435 ARG 0.007 0.000 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 12) link_NAG-ASN : angle 1.77224 ( 36) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 1.30211 ( 12) hydrogen bonds : bond 0.05165 ( 952) hydrogen bonds : angle 4.39646 ( 2691) SS BOND : bond 0.00303 ( 22) SS BOND : angle 1.35464 ( 44) covalent geometry : bond 0.00327 (21865) covalent geometry : angle 0.53038 (29710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7790.12 seconds wall clock time: 137 minutes 22.86 seconds (8242.86 seconds total)