Starting phenix.real_space_refine on Thu Jul 2 17:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gse_51545/07_2026/9gse_51545.map" } resolution = 3.64 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= -0.000 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 5839 2.51 5 N 1534 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9155 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7329 Classifications: {'peptide': 942} Link IDs: {'PTRANS': 45, 'TRANS': 896} Chain breaks: 2 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'KXP': 1} Classifications: {'undetermined': 1} 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 Time building chain proxies: 2.05, per 1000 atoms: 0.22 Number of scatterers: 9155 At special positions: 0 Unit cell: (93.73, 142.87, 157.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 3 15.00 O 1726 8.00 N 1534 7.00 C 5839 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 283 " " NAG B 502 " - " ASN B 295 " " NAG B 503 " - " ASN B 316 " " NAG B 504 " - " ASN B 170 " " NAG B 505 " - " ASN B 228 " " NAG B 506 " - " ASN B 196 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 300.6 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 48.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.635A pdb=" N MET A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.565A 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 103 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 150 through 189 removed outlier: 4.285A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.848A pdb=" N PHE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 377 removed outlier: 3.835A pdb=" N LYS A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.515A 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: 3.846A pdb=" N THR A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 445' 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 481 through 485 removed outlier: 3.587A pdb=" N ILE A 485 " --> pdb=" O PRO A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.876A pdb=" N LYS A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 589' Processing helix chain 'A' and resid 604 through 623 removed outlier: 3.884A pdb=" N ASP A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Proline residue: A 618 - end of helix 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 removed outlier: 3.591A pdb=" N LYS A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.625A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Proline residue: A 738 - end of helix No H-bonds generated for 'chain 'A' and resid 735 through 740' Processing helix chain 'A' and resid 747 through 760 Processing helix chain 'A' and resid 779 through 786 removed outlier: 3.785A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 803 removed outlier: 3.648A pdb=" N ALA A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 850 removed outlier: 4.217A pdb=" N ILE A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 861 through 881 removed outlier: 4.276A pdb=" N PHE A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.644A pdb=" N LEU A 890 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.809A pdb=" N MET A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 968 removed outlier: 3.704A pdb=" N ILE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.773A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.584A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A1037 " --> pdb=" O GLY A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 338 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 203 removed outlier: 5.307A pdb=" N THR A 193 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 213 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 264 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU A 266 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP A 233 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A 268 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 231 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 229 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.787A 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 203 removed outlier: 5.307A pdb=" N THR A 193 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 213 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 264 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU A 266 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP A 233 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A 268 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 231 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 229 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.787A 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: 6.032A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N LEU A 743 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET A 684 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 476 removed outlier: 5.251A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N LEU A 652 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP A 633 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 656 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 629 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 553 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 5.251A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 654 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 593 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N CYS A 656 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.543A 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: 6.724A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 9.047A 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: 6.724A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA B 236 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR B 263 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 259 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N HIS B 242 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR B 257 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.076A 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: 6.297A pdb=" N GLU B 246 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ARG B 333 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 248 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1353 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: 1.29 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1509 1.29 - 1.42: 2205 1.42 - 1.55: 5509 1.55 - 1.68: 19 1.68 - 1.81: 84 Bond restraints: 9326 Sorted by residual: bond pdb=" C3 KXP A1401 " pdb=" C6 KXP A1401 " ideal model delta sigma weight residual 1.523 1.240 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C49 KXP A1401 " pdb=" O50 KXP A1401 " ideal model delta sigma weight residual 1.204 1.466 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C21 KXP A1401 " pdb=" C22 KXP A1401 " ideal model delta sigma weight residual 1.506 1.652 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O45 KXP A1401 " pdb=" P42 KXP A1401 " ideal model delta sigma weight residual 1.527 1.385 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" O43 KXP A1401 " pdb=" P42 KXP A1401 " ideal model delta sigma weight residual 1.527 1.394 0.133 2.00e-02 2.50e+03 4.43e+01 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.32: 12648 13.32 - 26.63: 2 26.63 - 39.95: 0 39.95 - 53.27: 0 53.27 - 66.59: 2 Bond angle restraints: 12652 Sorted by residual: angle pdb=" C5 KXP A1401 " pdb=" C3 KXP A1401 " pdb=" C6 KXP A1401 " ideal model delta sigma weight residual 112.30 178.89 -66.59 3.00e+00 1.11e-01 4.93e+02 angle pdb=" O48 KXP A1401 " pdb=" C49 KXP A1401 " pdb=" O50 KXP A1401 " ideal model delta sigma weight residual 123.72 179.63 -55.91 3.00e+00 1.11e-01 3.47e+02 angle pdb=" O24 KXP A1401 " pdb=" P25 KXP A1401 " pdb=" O28 KXP A1401 " ideal model delta sigma weight residual 90.95 110.79 -19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" O26 KXP A1401 " pdb=" P25 KXP A1401 " pdb=" O27 KXP A1401 " ideal model delta sigma weight residual 119.47 101.80 17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" CB MET A 570 " pdb=" CG MET A 570 " pdb=" SD MET A 570 " ideal model delta sigma weight residual 112.70 125.24 -12.54 3.00e+00 1.11e-01 1.75e+01 ... (remaining 12647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.22: 5601 30.22 - 60.44: 174 60.44 - 90.67: 6 90.67 - 120.89: 0 120.89 - 151.11: 3 Dihedral angle restraints: 5784 sinusoidal: 2439 harmonic: 3345 Sorted by residual: dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.20 -88.80 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" O20 KXP A1401 " pdb=" C21 KXP A1401 " pdb=" C22 KXP A1401 " pdb=" O48 KXP A1401 " ideal model delta sinusoidal sigma weight residual 51.71 -99.40 151.11 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C31 KXP A1401 " pdb=" C32 KXP A1401 " pdb=" O41 KXP A1401 " pdb=" P42 KXP A1401 " ideal model delta sinusoidal sigma weight residual -105.93 35.41 -141.34 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 5781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1049 0.042 - 0.085: 337 0.085 - 0.127: 99 0.127 - 0.169: 11 0.169 - 0.212: 6 Chirality restraints: 1502 Sorted by residual: chirality pdb=" C2 NAG B 501 " pdb=" C1 NAG B 501 " pdb=" C3 NAG B 501 " pdb=" N2 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.28 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C22 KXP A1401 " pdb=" C21 KXP A1401 " pdb=" C23 KXP A1401 " pdb=" O48 KXP A1401 " both_signs ideal model delta sigma weight residual False -2.41 -2.60 0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C30 KXP A1401 " pdb=" C29 KXP A1401 " pdb=" C31 KXP A1401 " pdb=" O47 KXP A1401 " both_signs ideal model delta sigma weight residual False -2.41 -2.60 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 1499 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 927 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL A 927 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 927 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 928 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 176 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" CD GLU A 176 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU A 176 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 176 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 830 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ILE A 830 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 830 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 831 " 0.011 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4868 2.98 - 3.46: 9600 3.46 - 3.94: 14170 3.94 - 4.42: 15751 4.42 - 4.90: 25889 Nonbonded interactions: 70278 Sorted by model distance: nonbonded pdb=" O THR A 773 " pdb=" OG1 THR A 773 " model vdw 2.504 3.040 nonbonded pdb=" O GLN A 188 " pdb=" OE1 GLN A 188 " model vdw 2.508 3.040 nonbonded pdb=" N GLU A 66 " pdb=" OE1 GLU A 66 " model vdw 2.510 3.120 nonbonded pdb=" O GLU A 207 " pdb=" OE1 GLU A 207 " model vdw 2.590 3.040 nonbonded pdb=" O ARG A 604 " pdb=" OD1 ASP A 607 " model vdw 2.591 3.040 ... (remaining 70273 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.007 0.283 9334 Z= 0.323 Angle : 1.154 66.585 12674 Z= 0.476 Chirality : 0.046 0.212 1502 Planarity : 0.005 0.037 1591 Dihedral : 13.524 151.112 3614 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 17.26 % Favored : 81.15 % 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: 1148 helix: 0.81 (0.23), residues: 494 sheet: 0.50 (0.36), residues: 179 loop : -0.55 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 208 TYR 0.024 0.001 TYR B 263 PHE 0.008 0.001 PHE A 192 TRP 0.014 0.001 TRP B 183 HIS 0.010 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.32 ( 9326) covalent geometry : angle 1.14909 / 0.47 (12652) SS BOND : bond 0.00503 / 0.26 ( 2) SS BOND : angle 0.95972 / 0.55 ( 4) hydrogen bonds : bond 0.14613 / 9.71 ( 452) hydrogen bonds : angle 6.51730 / 4.67 ( 1353) link_NAG-ASN : bond 0.00303 / 0.19 ( 6) link_NAG-ASN : angle 3.18670 / 1.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8685 (mmm) cc_final: 0.8354 (ptt) REVERT: A 281 GLN cc_start: 0.8724 (mp10) cc_final: 0.8428 (mp10) REVERT: A 440 ASP cc_start: 0.8051 (t0) cc_final: 0.7744 (t0) REVERT: A 464 MET cc_start: 0.7503 (mmp) cc_final: 0.7225 (mmm) REVERT: A 539 TYR cc_start: 0.7460 (p90) cc_final: 0.7211 (p90) REVERT: A 570 MET cc_start: 0.6727 (tmm) cc_final: 0.5826 (tpp) REVERT: A 613 LYS cc_start: 0.8588 (mptt) cc_final: 0.8375 (mmtm) REVERT: A 756 LYS cc_start: 0.8790 (tttt) cc_final: 0.8471 (ttpp) REVERT: B 208 ARG cc_start: 0.8291 (tpp80) cc_final: 0.8069 (ttm-80) REVERT: B 245 SER cc_start: 0.9162 (p) cc_final: 0.8871 (m) REVERT: B 333 ARG cc_start: 0.8476 (tpp80) cc_final: 0.7669 (mmt90) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.0957 time to fit residues: 20.2067 Evaluate side-chains 146 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 204 ILE 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: 30.0000 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.173530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100820 restraints weight = 13744.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102836 restraints weight = 9006.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102989 restraints weight = 6270.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103129 restraints weight = 5778.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103250 restraints weight = 5698.743| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9334 Z= 0.245 Angle : 0.692 8.757 12674 Z= 0.348 Chirality : 0.045 0.207 1502 Planarity : 0.004 0.041 1591 Dihedral : 9.899 157.734 1443 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.66 % Allowed : 14.48 % Favored : 80.85 % 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: 0.20 (0.24), residues: 1148 helix: 0.94 (0.23), residues: 498 sheet: 0.60 (0.38), residues: 169 loop : -0.86 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.009 0.001 TYR B 296 PHE 0.014 0.001 PHE A 717 TRP 0.011 0.001 TRP A 867 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 ( 9326) covalent geometry : angle 0.68588 / 0.35 (12652) SS BOND : bond 0.00452 / 0.24 ( 2) SS BOND : angle 0.56870 / 0.33 ( 4) hydrogen bonds : bond 0.07299 / 4.88 ( 452) hydrogen bonds : angle 5.05601 / 3.62 ( 1353) link_NAG-ASN : bond 0.00237 / 0.13 ( 6) link_NAG-ASN : angle 2.46512 / 1.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 ASP cc_start: 0.8108 (t0) cc_final: 0.7824 (t0) REVERT: A 464 MET cc_start: 0.7894 (mmp) cc_final: 0.7587 (mmm) REVERT: A 529 LEU cc_start: 0.9300 (mt) cc_final: 0.9033 (mt) REVERT: A 539 TYR cc_start: 0.7406 (p90) cc_final: 0.7178 (p90) REVERT: A 564 MET cc_start: 0.8021 (tmm) cc_final: 0.7218 (tmm) REVERT: A 570 MET cc_start: 0.6719 (tmm) cc_final: 0.5997 (tpp) REVERT: A 756 LYS cc_start: 0.8923 (tttt) cc_final: 0.8564 (ttpp) REVERT: A 856 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8014 (mm-40) REVERT: B 245 SER cc_start: 0.9095 (p) cc_final: 0.8817 (m) REVERT: B 333 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7706 (mmt90) outliers start: 47 outliers final: 33 residues processed: 181 average time/residue: 0.0860 time to fit residues: 22.0098 Evaluate side-chains 157 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 355 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104744 restraints weight = 13687.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107699 restraints weight = 9309.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108103 restraints weight = 5867.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108106 restraints weight = 5722.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108331 restraints weight = 5376.182| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9334 Z= 0.131 Angle : 0.618 10.072 12674 Z= 0.304 Chirality : 0.043 0.178 1502 Planarity : 0.004 0.046 1591 Dihedral : 9.408 152.701 1441 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.97 % Allowed : 15.67 % Favored : 80.36 % 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: 0.41 (0.25), residues: 1148 helix: 1.19 (0.23), residues: 499 sheet: 0.44 (0.38), residues: 168 loop : -0.73 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 203 TYR 0.017 0.001 TYR B 202 PHE 0.015 0.001 PHE A 192 TRP 0.007 0.001 TRP A 737 HIS 0.010 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9326) covalent geometry : angle 0.61230 / 0.30 (12652) SS BOND : bond 0.00474 / 0.25 ( 2) SS BOND : angle 0.50846 / 0.28 ( 4) hydrogen bonds : bond 0.06053 / 4.03 ( 452) hydrogen bonds : angle 4.64293 / 3.31 ( 1353) link_NAG-ASN : bond 0.00284 / 0.15 ( 6) link_NAG-ASN : angle 2.28473 / 1.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8460 (pt0) cc_final: 0.8144 (pt0) REVERT: A 440 ASP cc_start: 0.8107 (t0) cc_final: 0.7843 (t0) REVERT: A 464 MET cc_start: 0.7971 (mmp) cc_final: 0.7662 (mmm) REVERT: A 570 MET cc_start: 0.6651 (tmm) cc_final: 0.6066 (tmm) REVERT: A 657 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 756 LYS cc_start: 0.8744 (tttt) cc_final: 0.8408 (ttpp) REVERT: A 856 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: B 159 ARG cc_start: 0.7227 (tpp80) cc_final: 0.6987 (tpp80) REVERT: B 245 SER cc_start: 0.9144 (p) cc_final: 0.8819 (m) REVERT: B 333 ARG cc_start: 0.8516 (tpp80) cc_final: 0.7725 (mmt90) outliers start: 40 outliers final: 28 residues processed: 169 average time/residue: 0.0862 time to fit residues: 20.4185 Evaluate side-chains 156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102418 restraints weight = 13806.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106264 restraints weight = 9146.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106212 restraints weight = 5775.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106436 restraints weight = 5718.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106607 restraints weight = 5433.300| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9334 Z= 0.143 Angle : 0.609 10.530 12674 Z= 0.301 Chirality : 0.043 0.177 1502 Planarity : 0.004 0.034 1591 Dihedral : 9.260 151.490 1440 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.96 % Allowed : 16.37 % Favored : 78.67 % 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: 0.40 (0.25), residues: 1148 helix: 1.24 (0.23), residues: 497 sheet: 0.62 (0.38), residues: 168 loop : -0.86 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 203 TYR 0.021 0.001 TYR B 296 PHE 0.025 0.001 PHE A 228 TRP 0.009 0.001 TRP A 867 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9326) covalent geometry : angle 0.60417 / 0.30 (12652) SS BOND : bond 0.00546 / 0.29 ( 2) SS BOND : angle 0.50547 / 0.28 ( 4) hydrogen bonds : bond 0.05954 / 3.98 ( 452) hydrogen bonds : angle 4.55195 / 3.23 ( 1353) link_NAG-ASN : bond 0.00293 / 0.16 ( 6) link_NAG-ASN : angle 2.15894 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLN cc_start: 0.8909 (mm110) cc_final: 0.8277 (mp10) REVERT: A 440 ASP cc_start: 0.8095 (t0) cc_final: 0.7824 (t0) REVERT: A 570 MET cc_start: 0.6695 (tmm) cc_final: 0.6165 (tmm) REVERT: A 636 SER cc_start: 0.2977 (OUTLIER) cc_final: 0.2254 (p) REVERT: A 668 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8834 (t) REVERT: A 698 ILE cc_start: 0.9146 (tp) cc_final: 0.8849 (pt) REVERT: A 856 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: B 159 ARG cc_start: 0.7233 (tpp80) cc_final: 0.7022 (tpp80) REVERT: B 217 CYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5015 (p) REVERT: B 245 SER cc_start: 0.9153 (p) cc_final: 0.8819 (m) REVERT: B 333 ARG cc_start: 0.8506 (tpp80) cc_final: 0.7753 (mmt90) outliers start: 50 outliers final: 33 residues processed: 173 average time/residue: 0.0929 time to fit residues: 22.4074 Evaluate side-chains 164 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 5.9990 chunk 90 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 87 optimal weight: 0.0010 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN A 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105179 restraints weight = 13763.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108523 restraints weight = 8559.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109995 restraints weight = 6001.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110385 restraints weight = 4743.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110747 restraints weight = 4886.864| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9334 Z= 0.111 Angle : 0.571 10.187 12674 Z= 0.282 Chirality : 0.043 0.187 1502 Planarity : 0.004 0.040 1591 Dihedral : 8.834 149.681 1438 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.27 % Allowed : 17.86 % Favored : 78.87 % 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: 0.55 (0.25), residues: 1148 helix: 1.42 (0.24), residues: 501 sheet: 0.73 (0.39), residues: 162 loop : -0.88 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 203 TYR 0.018 0.001 TYR B 296 PHE 0.018 0.001 PHE A 192 TRP 0.007 0.001 TRP A 737 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 9326) covalent geometry : angle 0.56612 / 0.28 (12652) SS BOND : bond 0.00529 / 0.27 ( 2) SS BOND : angle 0.52447 / 0.29 ( 4) hydrogen bonds : bond 0.05025 / 3.34 ( 452) hydrogen bonds : angle 4.31640 / 3.06 ( 1353) link_NAG-ASN : bond 0.00329 / 0.18 ( 6) link_NAG-ASN : angle 2.10272 / 1.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.8826 (tt0) cc_final: 0.8390 (mt0) REVERT: A 265 MET cc_start: 0.7988 (mmp) cc_final: 0.7786 (mmt) REVERT: A 281 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8238 (mp10) REVERT: A 440 ASP cc_start: 0.8051 (t0) cc_final: 0.7749 (t0) REVERT: A 564 MET cc_start: 0.8128 (tmm) cc_final: 0.7537 (tmm) REVERT: A 570 MET cc_start: 0.6670 (tmm) cc_final: 0.6180 (tmm) REVERT: A 636 SER cc_start: 0.2782 (OUTLIER) cc_final: 0.2068 (p) REVERT: A 668 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8766 (t) REVERT: A 698 ILE cc_start: 0.9113 (tp) cc_final: 0.8811 (pt) REVERT: B 245 SER cc_start: 0.9199 (p) cc_final: 0.8879 (m) REVERT: B 333 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7773 (mmt90) outliers start: 33 outliers final: 21 residues processed: 166 average time/residue: 0.0863 time to fit residues: 20.1794 Evaluate side-chains 156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100926 restraints weight = 13822.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103544 restraints weight = 8481.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103480 restraints weight = 5837.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103629 restraints weight = 5674.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103787 restraints weight = 5382.272| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9334 Z= 0.186 Angle : 0.620 10.710 12674 Z= 0.309 Chirality : 0.044 0.192 1502 Planarity : 0.004 0.033 1591 Dihedral : 8.738 152.376 1436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.66 % Allowed : 16.77 % Favored : 78.57 % 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: 0.37 (0.25), residues: 1148 helix: 1.26 (0.23), residues: 494 sheet: 0.52 (0.38), residues: 168 loop : -0.89 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 203 TYR 0.020 0.001 TYR B 296 PHE 0.020 0.001 PHE A 228 TRP 0.010 0.001 TRP B 183 HIS 0.009 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 9326) covalent geometry : angle 0.61531 / 0.31 (12652) SS BOND : bond 0.00874 / 0.46 ( 2) SS BOND : angle 0.68974 / 0.39 ( 4) hydrogen bonds : bond 0.06053 / 4.06 ( 452) hydrogen bonds : angle 4.45788 / 3.15 ( 1353) link_NAG-ASN : bond 0.00268 / 0.15 ( 6) link_NAG-ASN : angle 2.01154 / 1.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8849 (ptt90) cc_final: 0.8637 (ptt90) REVERT: A 215 GLN cc_start: 0.8870 (tt0) cc_final: 0.8466 (mt0) REVERT: A 265 MET cc_start: 0.8088 (mmp) cc_final: 0.7782 (mmt) REVERT: A 440 ASP cc_start: 0.8141 (t0) cc_final: 0.7820 (t0) REVERT: A 570 MET cc_start: 0.6726 (tmm) cc_final: 0.6251 (tmm) REVERT: A 636 SER cc_start: 0.2779 (OUTLIER) cc_final: 0.2054 (p) REVERT: A 907 MET cc_start: 0.7512 (tpp) cc_final: 0.7275 (tpp) REVERT: B 245 SER cc_start: 0.9221 (p) cc_final: 0.8891 (m) REVERT: B 333 ARG cc_start: 0.8517 (tpp80) cc_final: 0.7773 (mmt90) outliers start: 47 outliers final: 36 residues processed: 164 average time/residue: 0.0986 time to fit residues: 22.9301 Evaluate side-chains 163 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101838 restraints weight = 13819.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105160 restraints weight = 7891.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107343 restraints weight = 5693.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108343 restraints weight = 4759.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109214 restraints weight = 4290.013| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9334 Z= 0.125 Angle : 0.600 10.549 12674 Z= 0.295 Chirality : 0.043 0.178 1502 Planarity : 0.004 0.033 1591 Dihedral : 8.307 150.450 1434 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.57 % Allowed : 18.35 % Favored : 78.08 % 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: 0.46 (0.25), residues: 1148 helix: 1.33 (0.24), residues: 502 sheet: 0.57 (0.38), residues: 167 loop : -0.88 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 203 TYR 0.020 0.001 TYR B 296 PHE 0.016 0.001 PHE A 192 TRP 0.008 0.001 TRP A 867 HIS 0.009 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9326) covalent geometry : angle 0.59618 / 0.29 (12652) SS BOND : bond 0.00705 / 0.37 ( 2) SS BOND : angle 0.59156 / 0.32 ( 4) hydrogen bonds : bond 0.05412 / 3.60 ( 452) hydrogen bonds : angle 4.31393 / 3.05 ( 1353) link_NAG-ASN : bond 0.00319 / 0.17 ( 6) link_NAG-ASN : angle 1.82756 / 0.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5611 (tt) REVERT: A 215 GLN cc_start: 0.8821 (tt0) cc_final: 0.8482 (mt0) REVERT: A 440 ASP cc_start: 0.8071 (t0) cc_final: 0.7739 (t0) REVERT: A 570 MET cc_start: 0.6744 (tmm) cc_final: 0.6322 (tmm) REVERT: A 636 SER cc_start: 0.2974 (OUTLIER) cc_final: 0.2306 (p) REVERT: A 698 ILE cc_start: 0.9103 (tp) cc_final: 0.8772 (pt) REVERT: A 907 MET cc_start: 0.7446 (tpp) cc_final: 0.7188 (tpp) REVERT: B 245 SER cc_start: 0.9213 (p) cc_final: 0.8864 (m) REVERT: B 333 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7812 (mmt90) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 0.0957 time to fit residues: 22.1901 Evaluate side-chains 158 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS A1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.173301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102370 restraints weight = 14051.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101712 restraints weight = 8814.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101140 restraints weight = 7084.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101717 restraints weight = 6181.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101784 restraints weight = 5855.607| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9334 Z= 0.207 Angle : 0.656 9.726 12674 Z= 0.329 Chirality : 0.045 0.232 1502 Planarity : 0.004 0.034 1591 Dihedral : 8.151 153.252 1434 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.66 % Allowed : 18.06 % Favored : 77.28 % 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: 0.24 (0.24), residues: 1148 helix: 1.16 (0.23), residues: 489 sheet: 0.39 (0.38), residues: 169 loop : -0.92 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 203 TYR 0.017 0.001 TYR B 296 PHE 0.018 0.001 PHE A 192 TRP 0.011 0.001 TRP B 183 HIS 0.009 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 ( 9326) covalent geometry : angle 0.65290 / 0.33 (12652) SS BOND : bond 0.00552 / 0.29 ( 2) SS BOND : angle 0.50509 / 0.29 ( 4) hydrogen bonds : bond 0.06558 / 4.39 ( 452) hydrogen bonds : angle 4.51033 / 3.19 ( 1353) link_NAG-ASN : bond 0.00357 / 0.19 ( 6) link_NAG-ASN : angle 1.81395 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5728 (tt) REVERT: A 215 GLN cc_start: 0.8865 (tt0) cc_final: 0.8477 (mt0) REVERT: A 440 ASP cc_start: 0.8187 (t0) cc_final: 0.7887 (t0) REVERT: A 570 MET cc_start: 0.6857 (tmm) cc_final: 0.6396 (tmm) REVERT: A 636 SER cc_start: 0.2621 (OUTLIER) cc_final: 0.1866 (p) REVERT: A 698 ILE cc_start: 0.9150 (tp) cc_final: 0.8850 (pt) REVERT: A 907 MET cc_start: 0.7634 (tpp) cc_final: 0.7395 (tpp) REVERT: B 245 SER cc_start: 0.9228 (p) cc_final: 0.8872 (m) REVERT: B 333 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7767 (mmt90) outliers start: 47 outliers final: 37 residues processed: 171 average time/residue: 0.0919 time to fit residues: 22.3986 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 86 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102500 restraints weight = 13682.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105643 restraints weight = 8631.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106720 restraints weight = 6014.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107633 restraints weight = 4958.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107802 restraints weight = 5279.052| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9334 Z= 0.125 Angle : 0.624 10.276 12674 Z= 0.305 Chirality : 0.044 0.179 1502 Planarity : 0.004 0.047 1591 Dihedral : 7.776 151.305 1434 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.37 % Allowed : 20.04 % Favored : 76.59 % 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: 0.39 (0.25), residues: 1148 helix: 1.33 (0.23), residues: 496 sheet: 0.33 (0.39), residues: 165 loop : -0.86 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 203 TYR 0.019 0.001 TYR B 296 PHE 0.014 0.001 PHE B 278 TRP 0.008 0.001 TRP A 867 HIS 0.031 0.002 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9326) covalent geometry : angle 0.62092 / 0.30 (12652) SS BOND : bond 0.00538 / 0.28 ( 2) SS BOND : angle 0.34746 / 0.20 ( 4) hydrogen bonds : bond 0.05601 / 3.73 ( 452) hydrogen bonds : angle 4.31906 / 3.06 ( 1353) link_NAG-ASN : bond 0.00366 / 0.19 ( 6) link_NAG-ASN : angle 1.83111 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5488 (tt) REVERT: A 207 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 215 GLN cc_start: 0.8868 (tt0) cc_final: 0.8512 (mt0) REVERT: A 440 ASP cc_start: 0.8116 (t0) cc_final: 0.7797 (t0) REVERT: A 570 MET cc_start: 0.6792 (tmm) cc_final: 0.6360 (tmm) REVERT: A 636 SER cc_start: 0.2867 (OUTLIER) cc_final: 0.2200 (p) REVERT: A 698 ILE cc_start: 0.9124 (tp) cc_final: 0.8802 (pt) REVERT: A 907 MET cc_start: 0.7427 (tpp) cc_final: 0.7160 (tpp) REVERT: B 245 SER cc_start: 0.9237 (p) cc_final: 0.8863 (m) REVERT: B 333 ARG cc_start: 0.8498 (tpp80) cc_final: 0.7776 (mmt90) outliers start: 34 outliers final: 26 residues processed: 161 average time/residue: 0.0941 time to fit residues: 21.6296 Evaluate side-chains 157 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108583 restraints weight = 13718.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107115 restraints weight = 8143.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107746 restraints weight = 6480.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107966 restraints weight = 5812.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108403 restraints weight = 5477.608| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9334 Z= 0.127 Angle : 0.633 11.463 12674 Z= 0.309 Chirality : 0.044 0.178 1502 Planarity : 0.004 0.033 1591 Dihedral : 7.592 150.834 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.37 % Allowed : 20.14 % Favored : 76.49 % 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: 0.46 (0.25), residues: 1148 helix: 1.41 (0.24), residues: 490 sheet: 0.34 (0.39), residues: 160 loop : -0.82 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 203 TYR 0.019 0.001 TYR B 296 PHE 0.011 0.001 PHE A1024 TRP 0.009 0.001 TRP B 183 HIS 0.010 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9326) covalent geometry : angle 0.62864 / 0.31 (12652) SS BOND : bond 0.00754 / 0.40 ( 2) SS BOND : angle 0.38041 / 0.22 ( 4) hydrogen bonds : bond 0.05286 / 3.53 ( 452) hydrogen bonds : angle 4.24553 / 3.01 ( 1353) link_NAG-ASN : bond 0.00341 / 0.18 ( 6) link_NAG-ASN : angle 2.07436 / 1.00 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5558 (tt) REVERT: A 207 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 440 ASP cc_start: 0.8117 (t0) cc_final: 0.7794 (t0) REVERT: A 570 MET cc_start: 0.6877 (tmm) cc_final: 0.6413 (tmm) REVERT: A 636 SER cc_start: 0.2482 (OUTLIER) cc_final: 0.1719 (p) REVERT: A 698 ILE cc_start: 0.9092 (tp) cc_final: 0.8810 (pt) REVERT: A 907 MET cc_start: 0.7432 (tpp) cc_final: 0.7160 (tpp) REVERT: B 194 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7225 (mpp-170) REVERT: B 245 SER cc_start: 0.9216 (p) cc_final: 0.8859 (m) REVERT: B 333 ARG cc_start: 0.8508 (tpp80) cc_final: 0.7796 (mmt90) outliers start: 34 outliers final: 31 residues processed: 157 average time/residue: 0.0829 time to fit residues: 18.6135 Evaluate side-chains 163 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101498 restraints weight = 13633.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105920 restraints weight = 8716.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107118 restraints weight = 5864.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107352 restraints weight = 4934.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107430 restraints weight = 5172.799| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9334 Z= 0.133 Angle : 0.624 11.016 12674 Z= 0.305 Chirality : 0.044 0.174 1502 Planarity : 0.004 0.033 1591 Dihedral : 7.532 150.813 1434 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.57 % Allowed : 20.14 % Favored : 76.29 % 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: 0.42 (0.25), residues: 1148 helix: 1.38 (0.24), residues: 494 sheet: 0.32 (0.39), residues: 164 loop : -0.86 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 203 TYR 0.018 0.001 TYR B 296 PHE 0.011 0.001 PHE A1024 TRP 0.012 0.001 TRP B 183 HIS 0.012 0.002 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9326) covalent geometry : angle 0.62012 / 0.30 (12652) SS BOND : bond 0.00654 / 0.34 ( 2) SS BOND : angle 0.81194 / 0.45 ( 4) hydrogen bonds : bond 0.05341 / 3.57 ( 452) hydrogen bonds : angle 4.25100 / 3.02 ( 1353) link_NAG-ASN : bond 0.00342 / 0.18 ( 6) link_NAG-ASN : angle 1.99350 / 0.98 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.92 seconds wall clock time: 34 minutes 36.82 seconds (2076.82 seconds total)