Starting phenix.real_space_refine on Thu Jul 2 17:22:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsh_51548/07_2026/9gsh_51548.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 6 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 5805 2.51 5 N 1524 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 4 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: 9117 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7258 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 45, 'TRANS': 889} Chain breaks: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ANP': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 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: 2.09, per 1000 atoms: 0.23 Number of scatterers: 9117 At special positions: 0 Unit cell: (83.72, 90.09, 186.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 54 16.00 P 6 15.00 Mg 1 11.99 O 1726 8.00 N 1524 7.00 C 5805 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=2.03 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: 0.97 Conformation dependent library (CDL) restraints added in 337.8 milliseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 46.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.876A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 removed outlier: 4.355A pdb=" N VAL A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.382A pdb=" N ILE A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.603A pdb=" N GLN A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.877A pdb=" N ILE A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.238A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 340 through 377 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 410 removed outlier: 3.696A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.824A pdb=" N MET A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix 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 489 through 499 Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.529A pdb=" N ARG A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.831A pdb=" N LEU A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 678 removed outlier: 3.717A pdb=" N ARG A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 729 through 735 removed outlier: 3.589A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 740 removed outlier: 3.620A pdb=" N LEU A 740 " --> pdb=" O TRP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 761 removed outlier: 3.716A pdb=" N HIS A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.774A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 Processing helix chain 'A' and resid 813 through 852 removed outlier: 3.858A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 881 removed outlier: 3.732A pdb=" N ALA A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 903 through 932 removed outlier: 6.188A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 968 removed outlier: 3.803A pdb=" N ILE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 983 Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.688A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.613A pdb=" N TRP A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 360 removed outlier: 4.087A pdb=" N ILE B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.423A pdb=" N LYS A 235 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 267 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP A 233 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 269 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 231 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A 271 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 229 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 273 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 227 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 275 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 225 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.423A pdb=" N LYS A 235 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 267 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP A 233 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 269 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 231 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A 271 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 229 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 273 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 227 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 275 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 225 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.049A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY A 774 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 773 " --> pdb=" O CYS A 452 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP A 454 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N LEU A 743 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 6.938A 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: 3.919A pdb=" N VAL A 467 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A 629 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL A 657 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 627 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 659 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG A 625 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 576 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 568 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 564 " --> pdb=" O LYS A 580 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 565 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 4.447A 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: 3.919A pdb=" N VAL A 467 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU A 652 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS A 656 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.520A 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: 5.970A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.302A 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: 5.970A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 236 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TYR B 263 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS B 259 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS B 242 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR B 257 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 3.775A 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: 4.007A pdb=" N VAL B 326 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS B 315 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1272 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: 1.57 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1496 1.28 - 1.41: 2120 1.41 - 1.54: 5553 1.54 - 1.68: 31 1.68 - 1.81: 86 Bond restraints: 9286 Sorted by residual: bond pdb=" C3 KXP A1304 " pdb=" C6 KXP A1304 " ideal model delta sigma weight residual 1.523 1.201 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C49 KXP A1304 " pdb=" O50 KXP A1304 " ideal model delta sigma weight residual 1.204 1.457 -0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N3B ANP A1301 " pdb=" PG ANP A1301 " ideal model delta sigma weight residual 1.795 1.628 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" O45 KXP A1304 " pdb=" P42 KXP A1304 " ideal model delta sigma weight residual 1.527 1.389 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C21 KXP A1304 " pdb=" C22 KXP A1304 " ideal model delta sigma weight residual 1.506 1.643 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 9281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.44: 12603 13.44 - 26.87: 2 26.87 - 40.31: 0 40.31 - 53.75: 0 53.75 - 67.18: 2 Bond angle restraints: 12607 Sorted by residual: angle pdb=" C5 KXP A1304 " pdb=" C3 KXP A1304 " pdb=" C6 KXP A1304 " ideal model delta sigma weight residual 112.30 179.48 -67.18 3.00e+00 1.11e-01 5.02e+02 angle pdb=" O48 KXP A1304 " pdb=" C49 KXP A1304 " pdb=" O50 KXP A1304 " ideal model delta sigma weight residual 123.72 178.27 -54.55 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O24 KXP A1304 " pdb=" P25 KXP A1304 " pdb=" O28 KXP A1304 " ideal model delta sigma weight residual 90.95 110.70 -19.75 3.00e+00 1.11e-01 4.33e+01 angle pdb=" O26 KXP A1304 " pdb=" P25 KXP A1304 " pdb=" O27 KXP A1304 " ideal model delta sigma weight residual 119.47 100.05 19.42 3.00e+00 1.11e-01 4.19e+01 angle pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " ideal model delta sigma weight residual 112.00 102.11 9.89 2.20e+00 2.07e-01 2.02e+01 ... (remaining 12602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.65: 5469 29.65 - 59.30: 268 59.30 - 88.95: 28 88.95 - 118.60: 1 118.60 - 148.25: 2 Dihedral angle restraints: 5768 sinusoidal: 2445 harmonic: 3323 Sorted by residual: dihedral pdb=" CA GLY A1005 " pdb=" C GLY A1005 " pdb=" N GLY A1006 " pdb=" CA GLY A1006 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C2 KXP A1304 " pdb=" C1 KXP A1304 " pdb=" C18 KXP A1304 " pdb=" O1 KXP A1304 " ideal model delta sinusoidal sigma weight residual -21.13 -169.38 148.25 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O20 KXP A1304 " pdb=" C21 KXP A1304 " pdb=" C22 KXP A1304 " pdb=" O48 KXP A1304 " ideal model delta sinusoidal sigma weight residual 51.71 179.40 -127.69 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 5765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1313 0.072 - 0.144: 174 0.144 - 0.216: 8 0.216 - 0.289: 1 0.289 - 0.361: 3 Chirality restraints: 1499 Sorted by residual: chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 316 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C22 KXP A1304 " pdb=" C21 KXP A1304 " pdb=" C23 KXP A1304 " pdb=" O48 KXP A1304 " both_signs ideal model delta sigma weight residual False -2.41 -2.75 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' ANP A1301 " pdb=" C2' ANP A1301 " pdb=" C4' ANP A1301 " pdb=" O3' ANP A1301 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1496 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 169 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C ALA A 169 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA A 169 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 170 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 163 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C CYS A 163 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS A 163 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 164 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 168 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C THR A 168 " -0.045 2.00e-02 2.50e+03 pdb=" O THR A 168 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 169 " 0.015 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 573 2.73 - 3.27: 9353 3.27 - 3.82: 14359 3.82 - 4.36: 16922 4.36 - 4.90: 29539 Nonbonded interactions: 70746 Sorted by model distance: nonbonded pdb=" OD2 ASP A 873 " pdb="CA CA A1302 " model vdw 2.190 3.250 nonbonded pdb=" ND2 ASN B 316 " pdb=" N2 NAG B 503 " model vdw 2.281 2.560 nonbonded pdb=" OE1 GLU A 412 " pdb="CA CA A1302 " model vdw 2.413 3.250 nonbonded pdb=" O VAL A 410 " pdb="CA CA A1302 " model vdw 2.437 3.250 nonbonded pdb=" OD1 ASN A 869 " pdb="CA CA A1302 " model vdw 2.456 3.250 ... (remaining 70741 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.008 0.322 9294 Z= 0.365 Angle : 1.172 67.184 12629 Z= 0.488 Chirality : 0.049 0.361 1499 Planarity : 0.007 0.104 1577 Dihedral : 16.766 148.251 3612 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 1.60 % Allowed : 19.18 % Favored : 79.22 % 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: -0.33 (0.26), residues: 1139 helix: 0.68 (0.25), residues: 461 sheet: -0.02 (0.41), residues: 169 loop : -1.09 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 38 TYR 0.017 0.002 TYR B 263 PHE 0.014 0.002 PHE A 228 TRP 0.015 0.002 TRP A 151 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.37 ( 9286) covalent geometry : angle 1.14458 / 0.48 (12607) SS BOND : bond 0.00236 / 0.12 ( 2) SS BOND : angle 1.10553 / 0.56 ( 4) hydrogen bonds : bond 0.14512 / 9.39 ( 430) hydrogen bonds : angle 7.31011 / 5.43 ( 1272) link_NAG-ASN : bond 0.00624 / 0.41 ( 6) link_NAG-ASN : angle 6.73615 / 5.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 GLU cc_start: 0.7899 (pp20) cc_final: 0.7410 (tp30) REVERT: A 570 MET cc_start: 0.6615 (mtt) cc_final: 0.6394 (mtt) REVERT: B 234 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6812 (mtmm) REVERT: B 246 GLU cc_start: 0.8350 (tp30) cc_final: 0.8125 (tp30) outliers start: 16 outliers final: 14 residues processed: 103 average time/residue: 0.0867 time to fit residues: 12.9018 Evaluate side-chains 102 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 183 GLN A 202 GLN A 468 GLN A 500 ASN A 730 GLN A 837 GLN B 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.238110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.179189 restraints weight = 9614.382| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.30 r_work: 0.3407 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9294 Z= 0.129 Angle : 0.601 13.840 12629 Z= 0.301 Chirality : 0.045 0.397 1499 Planarity : 0.005 0.066 1577 Dihedral : 11.388 137.062 1468 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 4.40 % Allowed : 15.58 % Favored : 80.02 % 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: 0.32 (0.26), residues: 1139 helix: 1.42 (0.24), residues: 471 sheet: 0.22 (0.41), residues: 168 loop : -0.95 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.010 0.001 TYR A 218 PHE 0.011 0.001 PHE A 717 TRP 0.025 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9286) covalent geometry : angle 0.57503 / 0.30 (12607) SS BOND : bond 0.00328 / 0.16 ( 2) SS BOND : angle 0.75028 / 0.43 ( 4) hydrogen bonds : bond 0.05632 / 3.88 ( 430) hydrogen bonds : angle 4.82466 / 3.60 ( 1272) link_NAG-ASN : bond 0.00318 / 0.18 ( 6) link_NAG-ASN : angle 4.65848 / 3.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 622 ASP cc_start: 0.7044 (m-30) cc_final: 0.6520 (m-30) REVERT: B 234 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7061 (mtmm) outliers start: 44 outliers final: 29 residues processed: 122 average time/residue: 0.0738 time to fit residues: 13.2344 Evaluate side-chains 115 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 500 ASN A 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.238130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.179960 restraints weight = 9613.249| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.44 r_work: 0.3375 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9294 Z= 0.130 Angle : 0.573 10.983 12629 Z= 0.287 Chirality : 0.045 0.336 1499 Planarity : 0.004 0.042 1577 Dihedral : 10.388 133.331 1456 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.90 % Allowed : 15.28 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1139 helix: 1.63 (0.25), residues: 471 sheet: 0.42 (0.43), residues: 154 loop : -0.94 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.008 0.001 TYR B 359 PHE 0.011 0.001 PHE A 833 TRP 0.018 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9286) covalent geometry : angle 0.55079 / 0.28 (12607) SS BOND : bond 0.00376 / 0.19 ( 2) SS BOND : angle 0.52654 / 0.34 ( 4) hydrogen bonds : bond 0.05579 / 3.82 ( 430) hydrogen bonds : angle 4.59750 / 3.43 ( 1272) link_NAG-ASN : bond 0.00371 / 0.21 ( 6) link_NAG-ASN : angle 4.21245 / 3.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.5416 (ppp) cc_final: 0.5029 (ppp) REVERT: A 111 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7188 (mp) REVERT: A 412 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: B 234 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7115 (mtmm) outliers start: 49 outliers final: 33 residues processed: 128 average time/residue: 0.0846 time to fit residues: 16.0909 Evaluate side-chains 121 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 66 optimal weight: 0.0980 chunk 86 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 468 GLN A 495 ASN B 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.242173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170833 restraints weight = 9792.393| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.17 r_work: 0.3445 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9294 Z= 0.102 Angle : 0.519 8.337 12629 Z= 0.263 Chirality : 0.043 0.341 1499 Planarity : 0.004 0.034 1577 Dihedral : 9.671 111.387 1452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.40 % Allowed : 17.38 % Favored : 79.22 % 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: 0.71 (0.26), residues: 1139 helix: 1.84 (0.25), residues: 478 sheet: 0.32 (0.42), residues: 165 loop : -0.85 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.006 0.001 TYR B 180 PHE 0.008 0.001 PHE A1024 TRP 0.016 0.001 TRP A 151 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 9286) covalent geometry : angle 0.50425 / 0.26 (12607) SS BOND : bond 0.00360 / 0.18 ( 2) SS BOND : angle 1.06924 / 0.66 ( 4) hydrogen bonds : bond 0.04294 / 2.95 ( 430) hydrogen bonds : angle 4.41682 / 3.30 ( 1272) link_NAG-ASN : bond 0.00474 / 0.26 ( 6) link_NAG-ASN : angle 3.30539 / 2.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7244 (mp) REVERT: A 412 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: A 443 GLU cc_start: 0.7956 (pp20) cc_final: 0.7546 (tp30) REVERT: A 622 ASP cc_start: 0.7313 (t0) cc_final: 0.6745 (m-30) REVERT: B 205 ASN cc_start: 0.6851 (p0) cc_final: 0.6501 (t0) REVERT: B 234 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6687 (ptpp) REVERT: B 279 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6692 (mm-30) REVERT: B 296 TYR cc_start: 0.8045 (t80) cc_final: 0.7336 (t80) outliers start: 34 outliers final: 23 residues processed: 125 average time/residue: 0.0769 time to fit residues: 14.3792 Evaluate side-chains 110 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 545 GLN A 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.236563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3938 r_free = 0.3938 target = 0.158562 restraints weight = 9637.735| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.98 r_work: 0.3352 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9294 Z= 0.155 Angle : 0.568 8.197 12629 Z= 0.290 Chirality : 0.045 0.306 1499 Planarity : 0.004 0.038 1577 Dihedral : 9.710 114.960 1452 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.40 % Allowed : 16.68 % Favored : 78.92 % 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: 0.47 (0.26), residues: 1139 helix: 1.66 (0.25), residues: 475 sheet: 0.19 (0.42), residues: 170 loop : -1.00 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 892 TYR 0.010 0.001 TYR B 359 PHE 0.015 0.002 PHE A 833 TRP 0.014 0.001 TRP A 173 HIS 0.002 0.001 HIS A 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 ( 9286) covalent geometry : angle 0.55349 / 0.29 (12607) SS BOND : bond 0.00260 / 0.12 ( 2) SS BOND : angle 1.21225 / 0.74 ( 4) hydrogen bonds : bond 0.05979 / 4.10 ( 430) hydrogen bonds : angle 4.50489 / 3.36 ( 1272) link_NAG-ASN : bond 0.00614 / 0.34 ( 6) link_NAG-ASN : angle 3.39081 / 2.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 151 TRP cc_start: 0.7870 (p-90) cc_final: 0.7470 (p-90) REVERT: A 443 GLU cc_start: 0.7969 (pp20) cc_final: 0.7532 (tp30) REVERT: A 622 ASP cc_start: 0.7284 (t0) cc_final: 0.6702 (m-30) REVERT: B 205 ASN cc_start: 0.6913 (p0) cc_final: 0.6556 (t0) REVERT: B 234 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6579 (ptpp) outliers start: 44 outliers final: 36 residues processed: 122 average time/residue: 0.0709 time to fit residues: 12.8912 Evaluate side-chains 120 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.236303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.173197 restraints weight = 9633.016| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.91 r_work: 0.3294 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9294 Z= 0.142 Angle : 0.547 8.207 12629 Z= 0.280 Chirality : 0.044 0.290 1499 Planarity : 0.004 0.038 1577 Dihedral : 9.576 113.626 1452 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.20 % Allowed : 17.08 % Favored : 78.72 % 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: 0.45 (0.26), residues: 1139 helix: 1.64 (0.25), residues: 475 sheet: 0.13 (0.41), residues: 174 loop : -0.98 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.009 0.001 TYR B 359 PHE 0.013 0.001 PHE A 833 TRP 0.013 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9286) covalent geometry : angle 0.53518 / 0.28 (12607) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 0.99476 / 0.63 ( 4) hydrogen bonds : bond 0.05759 / 3.95 ( 430) hydrogen bonds : angle 4.48826 / 3.34 ( 1272) link_NAG-ASN : bond 0.00568 / 0.32 ( 6) link_NAG-ASN : angle 3.04732 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 151 TRP cc_start: 0.8010 (p-90) cc_final: 0.7598 (p-90) REVERT: A 546 MET cc_start: 0.6927 (tpt) cc_final: 0.6608 (tpt) REVERT: A 622 ASP cc_start: 0.7304 (t0) cc_final: 0.6691 (m-30) REVERT: B 205 ASN cc_start: 0.6727 (p0) cc_final: 0.6499 (t0) REVERT: B 234 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6898 (ptpp) outliers start: 42 outliers final: 31 residues processed: 117 average time/residue: 0.0735 time to fit residues: 12.7173 Evaluate side-chains 113 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.234638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173207 restraints weight = 9667.100| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.71 r_work: 0.3290 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9294 Z= 0.193 Angle : 0.580 8.906 12629 Z= 0.301 Chirality : 0.046 0.255 1499 Planarity : 0.004 0.041 1577 Dihedral : 9.709 123.696 1452 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.70 % Allowed : 16.68 % Favored : 78.62 % 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: 0.27 (0.26), residues: 1139 helix: 1.51 (0.25), residues: 469 sheet: 0.16 (0.43), residues: 160 loop : -1.09 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.011 0.001 TYR B 359 PHE 0.016 0.002 PHE A 932 TRP 0.012 0.001 TRP A 173 HIS 0.003 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 ( 9286) covalent geometry : angle 0.57113 / 0.30 (12607) SS BOND : bond 0.00204 / 0.10 ( 2) SS BOND : angle 1.03153 / 0.66 ( 4) hydrogen bonds : bond 0.06916 / 4.75 ( 430) hydrogen bonds : angle 4.58808 / 3.40 ( 1272) link_NAG-ASN : bond 0.00592 / 0.34 ( 6) link_NAG-ASN : angle 2.71648 / 1.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5569 (ppp) cc_final: 0.5083 (ppp) REVERT: A 151 TRP cc_start: 0.8240 (p-90) cc_final: 0.7783 (p-90) REVERT: B 205 ASN cc_start: 0.6611 (p0) cc_final: 0.6386 (t0) REVERT: B 234 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6933 (ptpp) outliers start: 47 outliers final: 39 residues processed: 122 average time/residue: 0.0715 time to fit residues: 12.8441 Evaluate side-chains 122 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 106 optimal weight: 0.0670 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.236773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165555 restraints weight = 9542.422| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.33 r_work: 0.3342 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9294 Z= 0.120 Angle : 0.523 8.317 12629 Z= 0.271 Chirality : 0.043 0.258 1499 Planarity : 0.004 0.038 1577 Dihedral : 9.388 116.252 1452 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.30 % Allowed : 18.18 % Favored : 78.52 % 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: 0.43 (0.26), residues: 1139 helix: 1.64 (0.25), residues: 474 sheet: 0.14 (0.43), residues: 164 loop : -1.00 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.008 0.001 TYR B 359 PHE 0.012 0.001 PHE A 836 TRP 0.011 0.001 TRP A 173 HIS 0.002 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9286) covalent geometry : angle 0.51382 / 0.27 (12607) SS BOND : bond 0.00307 / 0.15 ( 2) SS BOND : angle 0.90386 / 0.58 ( 4) hydrogen bonds : bond 0.05348 / 3.67 ( 430) hydrogen bonds : angle 4.46432 / 3.31 ( 1272) link_NAG-ASN : bond 0.00557 / 0.32 ( 6) link_NAG-ASN : angle 2.59584 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5697 (ppp) cc_final: 0.5231 (ppp) REVERT: A 111 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A 412 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: B 205 ASN cc_start: 0.6712 (p0) cc_final: 0.6258 (t0) REVERT: B 234 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6737 (ptpp) outliers start: 33 outliers final: 23 residues processed: 110 average time/residue: 0.0808 time to fit residues: 13.2013 Evaluate side-chains 107 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.240226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182522 restraints weight = 9796.627| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.37 r_work: 0.3423 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9294 Z= 0.108 Angle : 0.503 8.039 12629 Z= 0.259 Chirality : 0.043 0.250 1499 Planarity : 0.004 0.037 1577 Dihedral : 9.011 107.995 1452 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.50 % Allowed : 18.98 % Favored : 78.52 % 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: 0.66 (0.26), residues: 1139 helix: 1.80 (0.24), residues: 479 sheet: 0.21 (0.43), residues: 164 loop : -0.83 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.008 0.001 TYR B 359 PHE 0.011 0.001 PHE A1024 TRP 0.020 0.001 TRP A 151 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9286) covalent geometry : angle 0.49506 / 0.26 (12607) SS BOND : bond 0.00347 / 0.17 ( 2) SS BOND : angle 0.84744 / 0.55 ( 4) hydrogen bonds : bond 0.04662 / 3.21 ( 430) hydrogen bonds : angle 4.35378 / 3.23 ( 1272) link_NAG-ASN : bond 0.00546 / 0.31 ( 6) link_NAG-ASN : angle 2.42821 / 1.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5562 (ppp) cc_final: 0.5089 (ppp) REVERT: A 111 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 412 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: A 443 GLU cc_start: 0.7865 (pp20) cc_final: 0.7555 (tp30) REVERT: B 205 ASN cc_start: 0.6547 (p0) cc_final: 0.6245 (t0) REVERT: B 234 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6964 (ptpp) REVERT: B 279 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6626 (mm-30) outliers start: 25 outliers final: 21 residues processed: 104 average time/residue: 0.0855 time to fit residues: 12.9940 Evaluate side-chains 106 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.237860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163234 restraints weight = 9600.148| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.99 r_work: 0.3393 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9294 Z= 0.133 Angle : 0.524 8.346 12629 Z= 0.270 Chirality : 0.044 0.234 1499 Planarity : 0.004 0.039 1577 Dihedral : 8.986 108.964 1451 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.90 % Allowed : 18.78 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1139 helix: 1.82 (0.25), residues: 469 sheet: 0.19 (0.43), residues: 164 loop : -0.88 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.010 0.001 TYR B 359 PHE 0.012 0.001 PHE A 833 TRP 0.018 0.001 TRP A 151 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9286) covalent geometry : angle 0.51649 / 0.27 (12607) SS BOND : bond 0.00318 / 0.15 ( 2) SS BOND : angle 0.89802 / 0.59 ( 4) hydrogen bonds : bond 0.05486 / 3.78 ( 430) hydrogen bonds : angle 4.38763 / 3.25 ( 1272) link_NAG-ASN : bond 0.00557 / 0.32 ( 6) link_NAG-ASN : angle 2.34563 / 1.60 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5722 (ppp) cc_final: 0.5265 (ppp) REVERT: A 111 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7103 (mp) REVERT: A 443 GLU cc_start: 0.7961 (pp20) cc_final: 0.7521 (tp30) REVERT: A 546 MET cc_start: 0.7239 (tpt) cc_final: 0.6967 (tpt) REVERT: B 205 ASN cc_start: 0.6796 (p0) cc_final: 0.6291 (t0) REVERT: B 234 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6618 (ptpp) outliers start: 29 outliers final: 26 residues processed: 105 average time/residue: 0.0884 time to fit residues: 13.4912 Evaluate side-chains 109 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 312 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 61 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.237107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.176831 restraints weight = 9625.714| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.45 r_work: 0.3351 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9294 Z= 0.152 Angle : 0.534 8.788 12629 Z= 0.277 Chirality : 0.044 0.223 1499 Planarity : 0.004 0.039 1577 Dihedral : 8.977 111.791 1451 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.20 % Allowed : 18.48 % Favored : 78.32 % 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: 0.48 (0.26), residues: 1139 helix: 1.68 (0.25), residues: 475 sheet: 0.20 (0.43), residues: 164 loop : -0.99 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.010 0.001 TYR B 359 PHE 0.013 0.001 PHE A 932 TRP 0.017 0.001 TRP A 151 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 9286) covalent geometry : angle 0.52710 / 0.28 (12607) SS BOND : bond 0.00295 / 0.14 ( 2) SS BOND : angle 0.95610 / 0.63 ( 4) hydrogen bonds : bond 0.05969 / 4.11 ( 430) hydrogen bonds : angle 4.43710 / 3.28 ( 1272) link_NAG-ASN : bond 0.00578 / 0.33 ( 6) link_NAG-ASN : angle 2.27241 / 1.54 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2655.39 seconds wall clock time: 46 minutes 5.18 seconds (2765.18 seconds total)