Starting phenix.real_space_refine on Wed Aug 5 10:29:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsh_51548/08_2026/9gsh_51548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsh_51548/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsh_51548/08_2026/9gsh_51548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsh_51548/08_2026/9gsh_51548.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsh_51548/08_2026/9gsh_51548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsh_51548/08_2026/9gsh_51548.cif" } 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-2.2rc3-6140/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, 72 Unusual residues: {' CA': 1, ' MG': 1, 'ANP': 1, 'KXP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1.65, per 1000 atoms: 0.18 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: 0.55 Conformation dependent library (CDL) restraints added in 302.1 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: 0.26 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: 1.31 Time building geometry restraints manager: 0.71 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 2.510 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 2.510 nonbonded pdb=" O VAL A 410 " pdb="CA CA A1302 " model vdw 2.437 2.510 nonbonded pdb=" OD1 ASN A 869 " pdb="CA CA A1302 " model vdw 2.456 2.510 ... (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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- 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 : 0.328 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: 0.0724 time to fit residues: 10.8088 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 : 0.197 ------------------------------------------------------------------------------- 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 = 0.4599 r_free = 0.4599 target = 0.237914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170500 restraints weight = 9584.460| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.42 r_work: 0.3366 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0838 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 : 0.599 13.930 12629 Z= 0.300 Chirality : 0.045 0.397 1499 Planarity : 0.005 0.065 1577 Dihedral : 11.331 137.035 1468 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.50 % Allowed : 15.58 % Favored : 79.92 % 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: 0.31 (0.26), residues: 1139 helix: 1.41 (0.24), residues: 471 sheet: 0.22 (0.41), residues: 167 loop : -0.95 (0.29), residues: 501 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 0.010 0.001 PHE A 717 TRP 0.026 0.001 TRP A 173 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9286) covalent geometry : angle 0.57289 / 0.29 (12607) SS BOND : bond 0.00335 / 0.16 ( 2) SS BOND : angle 0.78253 / 0.44 ( 4) hydrogen bonds : bond 0.05635 / 3.88 ( 430) hydrogen bonds : angle 4.83541 / 3.61 ( 1272) link_NAG-ASN : bond 0.00308 / 0.17 ( 6) link_NAG-ASN : angle 4.68865 / 3.60 ( 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 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.2552 (mmt) cc_final: 0.2101 (tpp) REVERT: A 622 ASP cc_start: 0.7097 (m-30) cc_final: 0.6536 (m-30) REVERT: B 234 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6593 (mtmm) outliers start: 45 outliers final: 31 residues processed: 123 average time/residue: 0.0858 time to fit residues: 15.4692 Evaluate side-chains 117 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 869 ASN Chi-restraints excluded: chain A residue 878 LEU 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: 0.6980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 500 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.236555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152967 restraints weight = 9787.333| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.44 r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1062 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= 0.146 Angle : 0.584 10.902 12629 Z= 0.294 Chirality : 0.045 0.337 1499 Planarity : 0.004 0.043 1577 Dihedral : 10.399 134.344 1456 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 4.90 % Allowed : 15.58 % Favored : 79.52 % 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: 0.35 (0.26), residues: 1139 helix: 1.55 (0.25), residues: 472 sheet: 0.38 (0.43), residues: 154 loop : -1.08 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.009 0.001 TYR B 359 PHE 0.013 0.001 PHE A 833 TRP 0.018 0.001 TRP A 173 HIS 0.002 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9286) covalent geometry : angle 0.56264 / 0.29 (12607) SS BOND : bond 0.00344 / 0.17 ( 2) SS BOND : angle 0.56937 / 0.37 ( 4) hydrogen bonds : bond 0.06025 / 4.12 ( 430) hydrogen bonds : angle 4.61568 / 3.45 ( 1272) link_NAG-ASN : bond 0.00371 / 0.21 ( 6) link_NAG-ASN : angle 4.16417 / 3.00 ( 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 : 0.327 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.5527 (ppp) cc_final: 0.5257 (ppp) REVERT: B 234 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6300 (mtmm) REVERT: B 279 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6649 (mm-30) outliers start: 49 outliers final: 37 residues processed: 128 average time/residue: 0.0735 time to fit residues: 13.8884 Evaluate side-chains 125 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 ILE 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 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: 5.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 545 GLN A 837 GLN B 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.233573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169937 restraints weight = 9742.333| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.53 r_work: 0.3269 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9294 Z= 0.224 Angle : 0.629 8.880 12629 Z= 0.324 Chirality : 0.048 0.317 1499 Planarity : 0.004 0.043 1577 Dihedral : 10.260 133.498 1453 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.69 % Allowed : 14.79 % Favored : 79.52 % 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: 0.08 (0.26), residues: 1139 helix: 1.25 (0.25), residues: 474 sheet: 0.28 (0.43), residues: 155 loop : -1.18 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.013 0.002 TYR B 359 PHE 0.015 0.002 PHE A 932 TRP 0.016 0.002 TRP A 173 HIS 0.003 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.22 ( 9286) covalent geometry : angle 0.61657 / 0.32 (12607) SS BOND : bond 0.00220 / 0.11 ( 2) SS BOND : angle 1.17305 / 0.74 ( 4) hydrogen bonds : bond 0.07554 / 5.18 ( 430) hydrogen bonds : angle 4.69536 / 3.49 ( 1272) link_NAG-ASN : bond 0.00563 / 0.30 ( 6) link_NAG-ASN : angle 3.28181 / 2.34 ( 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 144 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 622 ASP cc_start: 0.7339 (t0) cc_final: 0.6818 (m-30) REVERT: A 899 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: B 234 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7101 (ptpp) outliers start: 57 outliers final: 43 residues processed: 134 average time/residue: 0.0685 time to fit residues: 13.7176 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL 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 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 465 THR 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 585 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 654 CYS 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 899 LYS 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 Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.238479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174994 restraints weight = 9654.606| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.54 r_work: 0.3376 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1509 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= 0.114 Angle : 0.540 7.896 12629 Z= 0.276 Chirality : 0.044 0.307 1499 Planarity : 0.004 0.039 1577 Dihedral : 9.714 121.264 1452 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.60 % Allowed : 18.08 % 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: 0.45 (0.26), residues: 1139 helix: 1.66 (0.25), residues: 467 sheet: 0.27 (0.43), residues: 159 loop : -0.98 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.007 0.001 TYR B 359 PHE 0.010 0.001 PHE A1024 TRP 0.013 0.001 TRP A 173 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9286) covalent geometry : angle 0.52337 / 0.27 (12607) SS BOND : bond 0.00300 / 0.14 ( 2) SS BOND : angle 1.43093 / 0.84 ( 4) hydrogen bonds : bond 0.05198 / 3.57 ( 430) hydrogen bonds : angle 4.50069 / 3.36 ( 1272) link_NAG-ASN : bond 0.00654 / 0.36 ( 6) link_NAG-ASN : angle 3.53456 / 2.36 ( 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 123 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.7899 (ppp) cc_final: 0.7365 (ppp) REVERT: A 111 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7334 (mp) REVERT: A 443 GLU cc_start: 0.7970 (pp20) cc_final: 0.7569 (tp30) REVERT: A 570 MET cc_start: 0.6751 (mmm) cc_final: 0.6318 (mtt) REVERT: A 622 ASP cc_start: 0.7298 (t0) cc_final: 0.6826 (m-30) REVERT: B 234 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6930 (ptpp) REVERT: B 279 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6623 (mp0) outliers start: 36 outliers final: 28 residues processed: 118 average time/residue: 0.0755 time to fit residues: 13.2741 Evaluate side-chains 114 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 400 ILE 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 585 ILE Chi-restraints excluded: chain A residue 654 CYS 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 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 924 LEU 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 Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 35 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A 475 HIS A 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.238672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173613 restraints weight = 9774.020| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.45 r_work: 0.3354 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1726 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= 0.111 Angle : 0.530 7.988 12629 Z= 0.270 Chirality : 0.043 0.292 1499 Planarity : 0.004 0.037 1577 Dihedral : 9.367 109.869 1452 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.50 % Allowed : 18.08 % Favored : 78.42 % 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: 1.74 (0.25), residues: 479 sheet: 0.26 (0.43), residues: 163 loop : -0.87 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.008 0.001 TYR B 359 PHE 0.010 0.001 PHE A1024 TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9286) covalent geometry : angle 0.51646 / 0.27 (12607) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 0.96880 / 0.60 ( 4) hydrogen bonds : bond 0.04726 / 3.25 ( 430) hydrogen bonds : angle 4.47787 / 3.36 ( 1272) link_NAG-ASN : bond 0.00597 / 0.34 ( 6) link_NAG-ASN : angle 3.15939 / 2.12 ( 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 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7826 (ppp) cc_final: 0.7314 (ppp) REVERT: A 111 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 443 GLU cc_start: 0.7944 (pp20) cc_final: 0.7559 (tp30) REVERT: A 546 MET cc_start: 0.7010 (tpt) cc_final: 0.6790 (tpt) REVERT: A 622 ASP cc_start: 0.7261 (t0) cc_final: 0.6712 (t0) REVERT: B 234 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6837 (ptpp) outliers start: 35 outliers final: 25 residues processed: 114 average time/residue: 0.0795 time to fit residues: 13.2584 Evaluate side-chains 107 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 435 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 654 CYS 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 703 ILE 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 812 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 59 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.6639 > 50:) chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.234998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157859 restraints weight = 9581.050| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.49 r_work: 0.3290 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9294 Z= 0.156 Angle : 0.554 8.422 12629 Z= 0.286 Chirality : 0.045 0.264 1499 Planarity : 0.004 0.039 1577 Dihedral : 9.436 116.851 1452 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.00 % Allowed : 18.38 % Favored : 77.62 % 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: 0.40 (0.26), residues: 1139 helix: 1.60 (0.25), residues: 474 sheet: 0.19 (0.43), residues: 163 loop : -1.02 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.010 0.001 TYR B 359 PHE 0.013 0.001 PHE A 932 TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9286) covalent geometry : angle 0.54338 / 0.28 (12607) SS BOND : bond 0.00507 / 0.26 ( 2) SS BOND : angle 1.10896 / 0.69 ( 4) hydrogen bonds : bond 0.06089 / 4.18 ( 430) hydrogen bonds : angle 4.50863 / 3.36 ( 1272) link_NAG-ASN : bond 0.00600 / 0.34 ( 6) link_NAG-ASN : angle 2.92797 / 1.97 ( 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 122 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5710 (ppp) cc_final: 0.5246 (ppp) REVERT: A 271 MET cc_start: 0.3408 (tpt) cc_final: 0.3037 (tpt) REVERT: A 443 GLU cc_start: 0.8048 (pp20) cc_final: 0.7662 (tp30) REVERT: B 234 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6579 (ptpp) outliers start: 40 outliers final: 30 residues processed: 117 average time/residue: 0.0764 time to fit residues: 13.1024 Evaluate side-chains 113 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 654 CYS 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 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 312 GLU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.0010 chunk 36 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.240156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175779 restraints weight = 9522.953| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.46 r_work: 0.3396 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9294 Z= 0.107 Angle : 0.510 8.109 12629 Z= 0.262 Chirality : 0.043 0.259 1499 Planarity : 0.004 0.037 1577 Dihedral : 9.056 112.924 1452 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.20 % Allowed : 18.98 % Favored : 77.82 % 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: 0.68 (0.26), residues: 1139 helix: 1.82 (0.25), residues: 479 sheet: 0.21 (0.43), residues: 164 loop : -0.83 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.007 0.001 TYR B 359 PHE 0.010 0.001 PHE A1024 TRP 0.016 0.001 TRP A 151 HIS 0.002 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9286) covalent geometry : angle 0.49951 / 0.26 (12607) SS BOND : bond 0.00334 / 0.16 ( 2) SS BOND : angle 0.94014 / 0.59 ( 4) hydrogen bonds : bond 0.04557 / 3.14 ( 430) hydrogen bonds : angle 4.37964 / 3.26 ( 1272) link_NAG-ASN : bond 0.00571 / 0.32 ( 6) link_NAG-ASN : angle 2.71722 / 1.82 ( 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 114 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5635 (ppp) cc_final: 0.5151 (ppp) REVERT: A 35 MET cc_start: 0.7823 (ppp) cc_final: 0.7275 (ppp) REVERT: A 443 GLU cc_start: 0.7829 (pp20) cc_final: 0.7505 (tp30) REVERT: A 622 ASP cc_start: 0.7378 (t0) cc_final: 0.6734 (t0) REVERT: B 234 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6833 (ptpp) REVERT: B 279 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6619 (mp0) outliers start: 32 outliers final: 29 residues processed: 109 average time/residue: 0.0762 time to fit residues: 12.2592 Evaluate side-chains 110 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 272 VAL 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 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 812 ASN Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 924 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 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.237462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175462 restraints weight = 9766.170| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1956 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= 0.143 Angle : 0.537 8.479 12629 Z= 0.277 Chirality : 0.044 0.236 1499 Planarity : 0.004 0.039 1577 Dihedral : 9.022 113.671 1451 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.20 % Allowed : 19.08 % Favored : 77.72 % 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: 0.49 (0.26), residues: 1139 helix: 1.71 (0.25), residues: 474 sheet: 0.21 (0.43), residues: 164 loop : -1.01 (0.28), residues: 501 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 833 TRP 0.016 0.001 TRP A 151 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 9286) covalent geometry : angle 0.52823 / 0.28 (12607) SS BOND : bond 0.00333 / 0.16 ( 2) SS BOND : angle 0.97612 / 0.63 ( 4) hydrogen bonds : bond 0.05769 / 3.96 ( 430) hydrogen bonds : angle 4.41855 / 3.29 ( 1272) link_NAG-ASN : bond 0.00589 / 0.34 ( 6) link_NAG-ASN : angle 2.58918 / 1.74 ( 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 113 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5618 (ppp) cc_final: 0.5130 (ppp) REVERT: A 35 MET cc_start: 0.7862 (ppp) cc_final: 0.7252 (ppp) REVERT: A 443 GLU cc_start: 0.7921 (pp20) cc_final: 0.7637 (tp30) REVERT: B 234 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6877 (ptpp) REVERT: B 279 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6731 (mp0) outliers start: 32 outliers final: 29 residues processed: 108 average time/residue: 0.0682 time to fit residues: 10.8174 Evaluate side-chains 111 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 272 VAL 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 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 812 ASN 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 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 306 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.234584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159073 restraints weight = 9566.446| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.51 r_work: 0.3256 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9294 Z= 0.161 Angle : 0.551 8.566 12629 Z= 0.285 Chirality : 0.045 0.222 1499 Planarity : 0.004 0.039 1577 Dihedral : 9.070 120.921 1451 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.50 % Allowed : 18.98 % Favored : 77.52 % 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: 0.41 (0.26), residues: 1139 helix: 1.60 (0.25), residues: 475 sheet: 0.21 (0.43), residues: 164 loop : -1.02 (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 833 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 0.00397 / 0.16 ( 9286) covalent geometry : angle 0.54329 / 0.28 (12607) SS BOND : bond 0.00318 / 0.16 ( 2) SS BOND : angle 1.01342 / 0.66 ( 4) hydrogen bonds : bond 0.06222 / 4.28 ( 430) hydrogen bonds : angle 4.47957 / 3.32 ( 1272) link_NAG-ASN : bond 0.00615 / 0.35 ( 6) link_NAG-ASN : angle 2.49075 / 1.66 ( 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 115 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5796 (ppp) cc_final: 0.5333 (ppp) REVERT: A 763 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7618 (t-90) REVERT: B 234 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6544 (ptpp) outliers start: 35 outliers final: 32 residues processed: 110 average time/residue: 0.0870 time to fit residues: 13.9854 Evaluate side-chains 114 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 654 CYS 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 763 HIS 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 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 Chi-restraints excluded: chain B residue 346 LEU 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: 0.6980 chunk 17 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN B 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.237678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.179302 restraints weight = 9446.038| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.20 r_work: 0.3405 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2102 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= 0.124 Angle : 0.518 8.143 12629 Z= 0.268 Chirality : 0.043 0.228 1499 Planarity : 0.004 0.038 1577 Dihedral : 8.828 119.126 1451 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.60 % Allowed : 18.88 % Favored : 77.52 % 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: 0.52 (0.26), residues: 1139 helix: 1.69 (0.25), residues: 478 sheet: 0.23 (0.43), residues: 164 loop : -0.95 (0.29), residues: 497 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 A 833 TRP 0.018 0.001 TRP A 151 HIS 0.002 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 9286) covalent geometry : angle 0.50973 / 0.27 (12607) SS BOND : bond 0.00334 / 0.16 ( 2) SS BOND : angle 0.93817 / 0.61 ( 4) hydrogen bonds : bond 0.05316 / 3.66 ( 430) hydrogen bonds : angle 4.40711 / 3.27 ( 1272) link_NAG-ASN : bond 0.00595 / 0.34 ( 6) link_NAG-ASN : angle 2.43208 / 1.61 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.33 seconds wall clock time: 43 minutes 0.40 seconds (2580.40 seconds total)