Starting phenix.real_space_refine on Thu Jul 2 17:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsf_51546/07_2026/9gsf_51546.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 5857 2.51 5 N 1538 2.21 5 O 1739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7337 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 942, 7326 Classifications: {'peptide': 942} Link IDs: {'PTRANS': 45, 'TRANS': 896} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 942, 7326 Classifications: {'peptide': 942} Link IDs: {'PTRANS': 45, 'TRANS': 896} Chain breaks: 2 bond proxies already assigned to first conformer: 7446 Chain: "B" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1703 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' MG': 1, 'ANP': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 395 " occ=0.46 ... (20 atoms not shown) pdb=" CZ BPHE A 395 " occ=0.54 Time building chain proxies: 3.51, per 1000 atoms: 0.38 Number of scatterers: 9195 At special positions: 0 Unit cell: (118.3, 153.79, 129.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 1 11.99 O 1739 8.00 N 1538 7.00 C 5857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 315 " 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 NAG-ASN " NAG B 501 " - " ASN B 316 " " NAG B 502 " - " ASN B 295 " " NAG B 503 " - " ASN B 283 " " NAG B 504 " - " ASN B 170 " " NAG B 505 " - " ASN B 228 " " NAG B 506 " - " ASN B 196 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 569.9 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 48.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.898A pdb=" N SER A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.681A pdb=" N VAL A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.633A pdb=" N ILE A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.666A pdb=" N GLN A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 123 through 124 No H-bonds generated for 'chain 'A' and resid 123 through 124' Processing helix chain 'A' and resid 149 through 149 No H-bonds generated for 'chain 'A' and resid 149 through 149' Processing helix chain 'A' and resid 150 through 190 removed outlier: 4.068A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 276 through 279 removed outlier: 3.769A pdb=" N ASN A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.836A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 377 removed outlier: 3.921A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 410 removed outlier: 4.275A pdb=" N TYR A 391 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.549A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.754A pdb=" N THR A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 471 through 474 removed outlier: 4.029A pdb=" N VAL A 474 " --> pdb=" O VAL A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.956A pdb=" N LEU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 538 through 545 removed outlier: 4.527A pdb=" N VAL A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 4.207A pdb=" N LYS A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.817A pdb=" N GLU A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 644 through 649 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 689 through 701 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.901A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.854A pdb=" N LYS A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 786 removed outlier: 4.024A pdb=" N LEU A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 803 removed outlier: 3.691A pdb=" N ALA A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 855 removed outlier: 3.880A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 881 removed outlier: 4.065A pdb=" N PHE A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.900A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 933 removed outlier: 6.301A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 968 Processing helix chain 'A' and resid 980 through 983 removed outlier: 3.685A pdb=" N ARG A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 980 through 983' Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.750A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.848A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.593A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 204 removed outlier: 5.068A pdb=" N THR A 193 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 213 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 264 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU A 266 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP A 233 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 268 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY A 231 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 225 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 204 removed outlier: 5.068A pdb=" N THR A 193 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 213 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 264 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU A 266 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP A 233 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 268 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY A 231 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 225 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.301A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 743 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N MET A 684 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.625A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS A 553 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.625A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS A 592 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS A 656 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N LEU A 594 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N VAL A 658 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.524A pdb=" N ARG B 149 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.706A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.706A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA B 236 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR B 263 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS B 259 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS B 242 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR B 257 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 258 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 297 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.310A pdb=" N GLU B 246 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG B 333 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS B 248 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 311 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1333 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: 1.80 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1606 1.32 - 1.45: 2255 1.45 - 1.57: 5414 1.57 - 1.70: 9 1.70 - 1.82: 85 Bond restraints: 9369 Sorted by residual: bond pdb=" N3B ANP A1301 " pdb=" PG ANP A1301 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" O36 KXP A1303 " pdb=" P37 KXP A1303 " ideal model delta sigma weight residual 1.722 1.613 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O41 KXP A1303 " pdb=" P42 KXP A1303 " ideal model delta sigma weight residual 1.725 1.618 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O3A ANP A1301 " pdb=" PB ANP A1301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C32 KXP A1303 " pdb=" O41 KXP A1303 " ideal model delta sigma weight residual 1.394 1.467 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 12511 2.25 - 4.49: 164 4.49 - 6.74: 35 6.74 - 8.99: 4 8.99 - 11.24: 5 Bond angle restraints: 12719 Sorted by residual: angle pdb=" C MET A 35 " pdb=" N GLU A 36 " pdb=" CA GLU A 36 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" O24 KXP A1303 " pdb=" P25 KXP A1303 " pdb=" O28 KXP A1303 " ideal model delta sigma weight residual 90.95 101.70 -10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C CYS A 853 " pdb=" N ILE A 854 " pdb=" CA ILE A 854 " ideal model delta sigma weight residual 122.97 119.67 3.30 9.80e-01 1.04e+00 1.13e+01 angle pdb=" CA LYS A 45 " pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA MET A 570 " pdb=" CB MET A 570 " pdb=" CG MET A 570 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 12714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.78: 5563 31.78 - 63.55: 229 63.55 - 95.33: 25 95.33 - 127.10: 1 127.10 - 158.88: 2 Dihedral angle restraints: 5820 sinusoidal: 2471 harmonic: 3349 Sorted by residual: dihedral pdb=" O1A ANP A1301 " pdb=" O3A ANP A1301 " pdb=" PA ANP A1301 " pdb=" PB ANP A1301 " ideal model delta sinusoidal sigma weight residual 83.11 -75.77 158.88 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" O1B ANP A1301 " pdb=" N3B ANP A1301 " pdb=" PB ANP A1301 " pdb=" PG ANP A1301 " ideal model delta sinusoidal sigma weight residual 35.15 -169.05 -155.80 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O20 KXP A1303 " pdb=" C21 KXP A1303 " pdb=" C22 KXP A1303 " pdb=" O48 KXP A1303 " ideal model delta sinusoidal sigma weight residual 51.71 160.89 -109.18 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 5817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1331 0.069 - 0.137: 166 0.137 - 0.206: 9 0.206 - 0.274: 0 0.274 - 0.343: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" C3' ANP A1301 " pdb=" C2' ANP A1301 " pdb=" C4' ANP A1301 " pdb=" O3' ANP A1301 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C29 KXP A1303 " pdb=" C30 KXP A1303 " pdb=" C34 KXP A1303 " pdb=" O28 KXP A1303 " both_signs ideal model delta sigma weight residual False 2.46 2.65 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" C33 KXP A1303 " pdb=" C32 KXP A1303 " pdb=" C34 KXP A1303 " pdb=" O36 KXP A1303 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1504 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 829 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C SER A 829 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 829 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 830 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 848 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA A 848 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 848 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 849 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 826 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C VAL A 826 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 826 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 827 " 0.011 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 5925 3.04 - 3.50: 9120 3.50 - 3.97: 13687 3.97 - 4.43: 16186 4.43 - 4.90: 25378 Nonbonded interactions: 70296 Sorted by model distance: nonbonded pdb=" O THR A 773 " pdb=" OG1 THR A 773 " model vdw 2.569 3.040 nonbonded pdb=" C SER A 944 " pdb=" OG SER A 944 " model vdw 2.589 2.616 nonbonded pdb=" O ASN A 232 " pdb=" OD1 ASP A 233 " model vdw 2.600 3.040 nonbonded pdb=" O THR A 882 " pdb=" OG1 THR A 882 " model vdw 2.607 3.040 nonbonded pdb=" C SER A 583 " pdb=" OG SER A 583 " model vdw 2.611 2.616 ... (remaining 70291 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.165 9377 Z= 0.230 Angle : 0.711 11.236 12741 Z= 0.361 Chirality : 0.046 0.343 1507 Planarity : 0.005 0.045 1594 Dihedral : 16.741 158.879 3648 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.68 % Allowed : 17.54 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1151 helix: 0.12 (0.23), residues: 483 sheet: 0.71 (0.37), residues: 198 loop : -0.76 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 576 TYR 0.017 0.001 TYR B 296 PHE 0.014 0.002 PHE A 717 TRP 0.013 0.001 TRP B 183 HIS 0.004 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 9369) covalent geometry : angle 0.70814 / 0.36 (12719) SS BOND : bond 0.00394 / 0.21 ( 2) SS BOND : angle 0.63284 / 0.24 ( 4) hydrogen bonds : bond 0.16499 / 11.01 ( 438) hydrogen bonds : angle 7.10477 / 5.03 ( 1333) link_NAG-ASN : bond 0.00557 / 0.21 ( 6) link_NAG-ASN : angle 1.97265 / 1.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.4998 (tpt170) cc_final: 0.4491 (tpt90) REVERT: A 100 TRP cc_start: 0.8001 (t-100) cc_final: 0.7433 (t60) REVERT: A 248 VAL cc_start: 0.6893 (t) cc_final: 0.6606 (m) REVERT: A 259 LEU cc_start: 0.8058 (mt) cc_final: 0.7540 (tp) REVERT: A 370 TYR cc_start: 0.7322 (t80) cc_final: 0.6947 (t80) REVERT: A 380 LYS cc_start: 0.8076 (tptp) cc_final: 0.7828 (mtmt) REVERT: A 689 ASN cc_start: 0.7227 (p0) cc_final: 0.6819 (p0) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.0906 time to fit residues: 16.0649 Evaluate side-chains 124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 944 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 314 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 519 GLN A 856 GLN A1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105237 restraints weight = 17396.346| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.28 r_work: 0.2900 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9377 Z= 0.160 Angle : 0.624 10.300 12741 Z= 0.317 Chirality : 0.044 0.173 1507 Planarity : 0.004 0.045 1594 Dihedral : 11.967 159.805 1478 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 2.08 % Allowed : 17.05 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1151 helix: 1.01 (0.23), residues: 490 sheet: 0.69 (0.39), residues: 186 loop : -0.74 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 576 TYR 0.011 0.001 TYR A 827 PHE 0.023 0.002 PHE A 228 TRP 0.014 0.001 TRP A 867 HIS 0.003 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9369) covalent geometry : angle 0.61992 / 0.32 (12719) SS BOND : bond 0.00352 / 0.18 ( 2) SS BOND : angle 0.51916 / 0.22 ( 4) hydrogen bonds : bond 0.07195 / 4.61 ( 438) hydrogen bonds : angle 4.99676 / 3.54 ( 1333) link_NAG-ASN : bond 0.00448 / 0.18 ( 6) link_NAG-ASN : angle 1.98724 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.4925 (tpt170) cc_final: 0.4406 (tpt90) REVERT: A 100 TRP cc_start: 0.7967 (t-100) cc_final: 0.7346 (t60) REVERT: A 248 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6589 (m) REVERT: A 259 LEU cc_start: 0.7952 (mt) cc_final: 0.7690 (mm) REVERT: A 380 LYS cc_start: 0.8124 (tptp) cc_final: 0.7873 (mtmt) REVERT: A 536 ARG cc_start: 0.8575 (mtt180) cc_final: 0.7997 (mmp80) REVERT: A 689 ASN cc_start: 0.6573 (p0) cc_final: 0.6283 (p0) REVERT: B 309 ASP cc_start: 0.8700 (m-30) cc_final: 0.8489 (m-30) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 0.0909 time to fit residues: 16.7133 Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109090 restraints weight = 18085.788| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.32 r_work: 0.2974 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9377 Z= 0.127 Angle : 0.581 10.452 12741 Z= 0.292 Chirality : 0.043 0.178 1507 Planarity : 0.004 0.039 1594 Dihedral : 10.631 162.125 1462 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.98 % Allowed : 17.24 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1151 helix: 1.42 (0.23), residues: 491 sheet: 0.74 (0.39), residues: 186 loop : -0.68 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.016 0.001 TYR B 296 PHE 0.030 0.001 PHE A 228 TRP 0.012 0.001 TRP A 867 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9369) covalent geometry : angle 0.57753 / 0.29 (12719) SS BOND : bond 0.00368 / 0.19 ( 2) SS BOND : angle 0.59547 / 0.24 ( 4) hydrogen bonds : bond 0.05974 / 3.83 ( 438) hydrogen bonds : angle 4.49820 / 3.20 ( 1333) link_NAG-ASN : bond 0.00487 / 0.19 ( 6) link_NAG-ASN : angle 1.80273 / 0.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8188 (ttm170) REVERT: A 59 ARG cc_start: 0.5035 (tpt170) cc_final: 0.4491 (tpt90) REVERT: A 100 TRP cc_start: 0.7957 (t-100) cc_final: 0.7260 (t60) REVERT: A 104 GLN cc_start: 0.8185 (pt0) cc_final: 0.7738 (pm20) REVERT: A 248 VAL cc_start: 0.6902 (t) cc_final: 0.6670 (m) REVERT: A 259 LEU cc_start: 0.7796 (mt) cc_final: 0.7518 (mm) REVERT: A 380 LYS cc_start: 0.8133 (tptp) cc_final: 0.7909 (mtmt) REVERT: A 536 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8010 (mmp80) REVERT: A 689 ASN cc_start: 0.6284 (p0) cc_final: 0.6075 (p0) REVERT: A 779 ASP cc_start: 0.8362 (t0) cc_final: 0.8127 (t0) REVERT: A 1020 MET cc_start: 0.8262 (mmm) cc_final: 0.8051 (mmm) outliers start: 20 outliers final: 11 residues processed: 136 average time/residue: 0.0938 time to fit residues: 18.0575 Evaluate side-chains 123 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 966 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103115 restraints weight = 30533.777| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.23 r_work: 0.2835 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9377 Z= 0.166 Angle : 0.608 10.370 12741 Z= 0.308 Chirality : 0.044 0.182 1507 Planarity : 0.004 0.037 1594 Dihedral : 10.208 161.969 1458 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 2.87 % Allowed : 16.75 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1151 helix: 1.41 (0.23), residues: 491 sheet: 0.62 (0.39), residues: 181 loop : -0.74 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.016 0.001 TYR A 370 PHE 0.023 0.002 PHE A 228 TRP 0.015 0.001 TRP B 183 HIS 0.004 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9369) covalent geometry : angle 0.60527 / 0.31 (12719) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.64792 / 0.27 ( 4) hydrogen bonds : bond 0.06737 / 4.28 ( 438) hydrogen bonds : angle 4.51622 / 3.21 ( 1333) link_NAG-ASN : bond 0.00472 / 0.18 ( 6) link_NAG-ASN : angle 1.67588 / 0.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.386 Fit side-chains REVERT: A 59 ARG cc_start: 0.5010 (tpt170) cc_final: 0.4507 (tpt90) REVERT: A 100 TRP cc_start: 0.8028 (t-100) cc_final: 0.7701 (t60) REVERT: A 236 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 248 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6752 (m) REVERT: A 259 LEU cc_start: 0.8045 (mt) cc_final: 0.7758 (mm) REVERT: A 380 LYS cc_start: 0.8208 (tptp) cc_final: 0.7971 (mtmt) REVERT: A 478 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7462 (tm-30) REVERT: A 536 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8058 (mmp80) REVERT: A 689 ASN cc_start: 0.6585 (p0) cc_final: 0.6363 (p0) REVERT: A 902 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8830 (mm) REVERT: B 199 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6609 (m110) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 0.0950 time to fit residues: 18.2432 Evaluate side-chains 130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.177788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104389 restraints weight = 20527.140| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.17 r_work: 0.2936 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9377 Z= 0.132 Angle : 0.568 9.399 12741 Z= 0.287 Chirality : 0.043 0.174 1507 Planarity : 0.004 0.039 1594 Dihedral : 9.992 163.707 1458 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.78 % Allowed : 18.24 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1151 helix: 1.52 (0.23), residues: 491 sheet: 0.70 (0.39), residues: 187 loop : -0.76 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.017 0.001 TYR A 370 PHE 0.012 0.001 PHE A 717 TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9369) covalent geometry : angle 0.56543 / 0.29 (12719) SS BOND : bond 0.00259 / 0.14 ( 2) SS BOND : angle 0.69247 / 0.31 ( 4) hydrogen bonds : bond 0.05983 / 3.82 ( 438) hydrogen bonds : angle 4.34374 / 3.09 ( 1333) link_NAG-ASN : bond 0.00496 / 0.20 ( 6) link_NAG-ASN : angle 1.60890 / 0.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.360 Fit side-chains REVERT: A 32 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8443 (ttm110) REVERT: A 35 MET cc_start: 0.8509 (mmt) cc_final: 0.8294 (mmt) REVERT: A 59 ARG cc_start: 0.4993 (tpt170) cc_final: 0.4500 (tpt90) REVERT: A 100 TRP cc_start: 0.8008 (t-100) cc_final: 0.7339 (t60) REVERT: A 104 GLN cc_start: 0.8242 (pt0) cc_final: 0.7777 (pm20) REVERT: A 236 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6591 (mp) REVERT: A 248 VAL cc_start: 0.7142 (OUTLIER) cc_final: 0.6910 (m) REVERT: A 259 LEU cc_start: 0.7991 (mt) cc_final: 0.7697 (mm) REVERT: A 380 LYS cc_start: 0.8122 (tptp) cc_final: 0.7916 (mtmt) REVERT: A 478 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7449 (tm-30) REVERT: A 536 ARG cc_start: 0.8547 (mtt180) cc_final: 0.8101 (mmp-170) REVERT: A 1020 MET cc_start: 0.8319 (mmm) cc_final: 0.8108 (mmm) REVERT: B 199 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6631 (m110) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 0.0964 time to fit residues: 17.0139 Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106130 restraints weight = 18119.791| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.23 r_work: 0.2890 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9377 Z= 0.164 Angle : 0.593 9.537 12741 Z= 0.304 Chirality : 0.044 0.170 1507 Planarity : 0.004 0.040 1594 Dihedral : 9.923 162.734 1458 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 2.58 % Allowed : 17.64 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1151 helix: 1.48 (0.23), residues: 482 sheet: 0.82 (0.41), residues: 171 loop : -0.80 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.013 0.001 TYR B 296 PHE 0.016 0.001 PHE A 717 TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 9369) covalent geometry : angle 0.59012 / 0.30 (12719) SS BOND : bond 0.00244 / 0.13 ( 2) SS BOND : angle 0.62649 / 0.26 ( 4) hydrogen bonds : bond 0.06496 / 4.12 ( 438) hydrogen bonds : angle 4.40279 / 3.14 ( 1333) link_NAG-ASN : bond 0.00457 / 0.18 ( 6) link_NAG-ASN : angle 1.56965 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8374 (ttm110) REVERT: A 35 MET cc_start: 0.8454 (mmt) cc_final: 0.8244 (mmt) REVERT: A 59 ARG cc_start: 0.5012 (tpt170) cc_final: 0.4525 (tpt90) REVERT: A 100 TRP cc_start: 0.8078 (t-100) cc_final: 0.7167 (t60) REVERT: A 104 GLN cc_start: 0.8374 (pt0) cc_final: 0.7909 (pm20) REVERT: A 236 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6621 (mp) REVERT: A 248 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6872 (m) REVERT: A 259 LEU cc_start: 0.8064 (mt) cc_final: 0.7755 (mm) REVERT: A 380 LYS cc_start: 0.8175 (tptp) cc_final: 0.7969 (mtmt) REVERT: A 478 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7455 (tm-30) REVERT: A 536 ARG cc_start: 0.8506 (mtt180) cc_final: 0.8105 (mmp-170) REVERT: A 902 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8830 (mm) REVERT: B 232 GLU cc_start: 0.5647 (tm-30) cc_final: 0.5446 (tm-30) REVERT: B 263 TYR cc_start: 0.7027 (t80) cc_final: 0.6676 (t80) outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 0.0995 time to fit residues: 19.1476 Evaluate side-chains 131 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 108 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101680 restraints weight = 23789.163| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.60 r_work: 0.2877 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9377 Z= 0.152 Angle : 0.589 10.064 12741 Z= 0.299 Chirality : 0.043 0.168 1507 Planarity : 0.004 0.041 1594 Dihedral : 9.831 162.891 1458 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 2.68 % Allowed : 17.74 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1151 helix: 1.51 (0.23), residues: 482 sheet: 0.79 (0.40), residues: 171 loop : -0.81 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.014 0.001 TYR B 296 PHE 0.014 0.001 PHE A 717 TRP 0.012 0.001 TRP B 183 HIS 0.003 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9369) covalent geometry : angle 0.58696 / 0.30 (12719) SS BOND : bond 0.00248 / 0.13 ( 2) SS BOND : angle 0.62101 / 0.27 ( 4) hydrogen bonds : bond 0.06279 / 3.99 ( 438) hydrogen bonds : angle 4.34441 / 3.09 ( 1333) link_NAG-ASN : bond 0.00437 / 0.17 ( 6) link_NAG-ASN : angle 1.54909 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8365 (ttm110) REVERT: A 59 ARG cc_start: 0.4954 (tpt170) cc_final: 0.4490 (tpt90) REVERT: A 100 TRP cc_start: 0.8015 (t-100) cc_final: 0.7082 (t60) REVERT: A 104 GLN cc_start: 0.8384 (pt0) cc_final: 0.7873 (pm20) REVERT: A 236 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6616 (mp) REVERT: A 248 VAL cc_start: 0.7044 (OUTLIER) cc_final: 0.6788 (m) REVERT: A 259 LEU cc_start: 0.8076 (mt) cc_final: 0.7769 (mm) REVERT: A 380 LYS cc_start: 0.8144 (tptp) cc_final: 0.7938 (mtmt) REVERT: A 478 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7449 (tm-30) REVERT: A 536 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8028 (mmp80) REVERT: A 902 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8803 (mm) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.0995 time to fit residues: 17.8538 Evaluate side-chains 126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099996 restraints weight = 22026.823| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.48 r_work: 0.2841 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9377 Z= 0.181 Angle : 0.607 9.586 12741 Z= 0.313 Chirality : 0.044 0.173 1507 Planarity : 0.004 0.044 1594 Dihedral : 9.792 161.048 1458 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 2.48 % Allowed : 18.04 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1151 helix: 1.41 (0.23), residues: 482 sheet: 0.62 (0.40), residues: 173 loop : -0.85 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.013 0.001 TYR B 263 PHE 0.017 0.002 PHE A 717 TRP 0.013 0.001 TRP B 183 HIS 0.004 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9369) covalent geometry : angle 0.60478 / 0.31 (12719) SS BOND : bond 0.00207 / 0.11 ( 2) SS BOND : angle 0.58774 / 0.24 ( 4) hydrogen bonds : bond 0.06802 / 4.31 ( 438) hydrogen bonds : angle 4.42072 / 3.14 ( 1333) link_NAG-ASN : bond 0.00424 / 0.17 ( 6) link_NAG-ASN : angle 1.54489 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8388 (ttm110) REVERT: A 59 ARG cc_start: 0.4897 (tpt170) cc_final: 0.4439 (tpt90) REVERT: A 100 TRP cc_start: 0.8027 (t-100) cc_final: 0.7073 (t60) REVERT: A 104 GLN cc_start: 0.8414 (pt0) cc_final: 0.7895 (pm20) REVERT: A 236 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6585 (mp) REVERT: A 248 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6779 (m) REVERT: A 259 LEU cc_start: 0.8141 (mt) cc_final: 0.7823 (mm) REVERT: A 380 LYS cc_start: 0.8140 (tptp) cc_final: 0.7927 (mtmt) REVERT: A 478 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7372 (tm-30) REVERT: A 536 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8045 (mmp80) REVERT: A 902 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8830 (mm) outliers start: 25 outliers final: 19 residues processed: 128 average time/residue: 0.0975 time to fit residues: 17.6800 Evaluate side-chains 129 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 87 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106410 restraints weight = 27108.523| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.05 r_work: 0.2942 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9377 Z= 0.124 Angle : 0.570 10.562 12741 Z= 0.288 Chirality : 0.043 0.167 1507 Planarity : 0.004 0.040 1594 Dihedral : 9.635 161.669 1458 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 1.59 % Allowed : 19.33 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1151 helix: 1.54 (0.23), residues: 489 sheet: 0.96 (0.42), residues: 151 loop : -0.77 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.014 0.001 TYR B 296 PHE 0.011 0.001 PHE A 717 TRP 0.012 0.001 TRP A 737 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9369) covalent geometry : angle 0.56745 / 0.29 (12719) SS BOND : bond 0.00268 / 0.14 ( 2) SS BOND : angle 0.60757 / 0.28 ( 4) hydrogen bonds : bond 0.05617 / 3.58 ( 438) hydrogen bonds : angle 4.22958 / 3.00 ( 1333) link_NAG-ASN : bond 0.00442 / 0.18 ( 6) link_NAG-ASN : angle 1.52056 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8405 (ttm110) REVERT: A 59 ARG cc_start: 0.4922 (tpt170) cc_final: 0.4061 (tmt-80) REVERT: A 100 TRP cc_start: 0.8119 (t-100) cc_final: 0.7385 (t60) REVERT: A 104 GLN cc_start: 0.8469 (pt0) cc_final: 0.7962 (pm20) REVERT: A 236 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6732 (mp) REVERT: A 248 VAL cc_start: 0.7134 (t) cc_final: 0.6901 (m) REVERT: A 259 LEU cc_start: 0.8137 (mt) cc_final: 0.7714 (mm) REVERT: A 380 LYS cc_start: 0.8165 (tptp) cc_final: 0.7935 (mtmt) REVERT: A 478 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7419 (tm-30) REVERT: A 536 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8004 (mmp80) REVERT: A 546 MET cc_start: 0.8616 (mmt) cc_final: 0.8394 (tpp) REVERT: B 263 TYR cc_start: 0.6845 (t80) cc_final: 0.6631 (t80) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.0971 time to fit residues: 16.5235 Evaluate side-chains 119 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN B 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107208 restraints weight = 20649.492| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.75 r_work: 0.2992 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9377 Z= 0.121 Angle : 0.561 9.713 12741 Z= 0.285 Chirality : 0.042 0.167 1507 Planarity : 0.004 0.041 1594 Dihedral : 9.483 156.037 1458 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.49 % Allowed : 19.33 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1151 helix: 1.63 (0.23), residues: 488 sheet: 0.82 (0.39), residues: 175 loop : -0.80 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.014 0.001 TYR B 296 PHE 0.019 0.001 PHE B 221 TRP 0.012 0.001 TRP A 867 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9369) covalent geometry : angle 0.55906 / 0.28 (12719) SS BOND : bond 0.00239 / 0.12 ( 2) SS BOND : angle 0.56008 / 0.26 ( 4) hydrogen bonds : bond 0.05417 / 3.45 ( 438) hydrogen bonds : angle 4.13372 / 2.94 ( 1333) link_NAG-ASN : bond 0.00453 / 0.19 ( 6) link_NAG-ASN : angle 1.47804 / 0.78 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8407 (ttm110) REVERT: A 59 ARG cc_start: 0.4920 (tpt170) cc_final: 0.4083 (tmt-80) REVERT: A 100 TRP cc_start: 0.8024 (t-100) cc_final: 0.7311 (t60) REVERT: A 104 GLN cc_start: 0.8388 (pt0) cc_final: 0.7864 (pm20) REVERT: A 215 GLN cc_start: 0.8396 (tt0) cc_final: 0.8144 (tt0) REVERT: A 236 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6634 (mp) REVERT: A 248 VAL cc_start: 0.7088 (t) cc_final: 0.6860 (m) REVERT: A 259 LEU cc_start: 0.8025 (mt) cc_final: 0.7591 (mm) REVERT: A 380 LYS cc_start: 0.8149 (tptp) cc_final: 0.7926 (mtmt) REVERT: A 478 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7414 (tm-30) REVERT: A 536 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8012 (mmp80) REVERT: B 216 HIS cc_start: 0.7341 (m-70) cc_final: 0.6268 (t-90) outliers start: 15 outliers final: 9 residues processed: 124 average time/residue: 0.0971 time to fit residues: 16.8716 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105419 restraints weight = 17648.582| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.08 r_work: 0.3055 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9377 Z= 0.118 Angle : 0.564 10.211 12741 Z= 0.285 Chirality : 0.043 0.166 1507 Planarity : 0.004 0.041 1594 Dihedral : 9.162 147.198 1458 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 1.09 % Allowed : 19.62 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1151 helix: 1.70 (0.23), residues: 483 sheet: 0.90 (0.40), residues: 173 loop : -0.77 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 576 TYR 0.014 0.001 TYR B 296 PHE 0.020 0.001 PHE B 221 TRP 0.012 0.001 TRP A 867 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9369) covalent geometry : angle 0.56133 / 0.28 (12719) SS BOND : bond 0.00241 / 0.13 ( 2) SS BOND : angle 0.52366 / 0.24 ( 4) hydrogen bonds : bond 0.05213 / 3.31 ( 438) hydrogen bonds : angle 4.10027 / 2.92 ( 1333) link_NAG-ASN : bond 0.00465 / 0.19 ( 6) link_NAG-ASN : angle 1.46538 / 0.77 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.03 seconds wall clock time: 53 minutes 29.07 seconds (3209.07 seconds total)