Starting phenix.real_space_refine on Fri Jul 3 13:43:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmx_51457/07_2026/9gmx_51457.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 P 56 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 9043 2.51 5 N 2541 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14540 Number of models: 1 Model: "" Number of chains: 7 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "T" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1119 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 9, 'rna3p': 42} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2116 SG CYS A 287 73.645 72.496 74.308 1.00 66.00 S ATOM 2393 SG CYS A 321 73.307 73.871 77.836 1.00 51.75 S ATOM 2399 SG CYS A 322 70.876 71.223 76.566 1.00 63.51 S ATOM 8781 SG CYS B 287 22.770 59.894 73.562 1.00 73.92 S ATOM 9058 SG CYS B 321 23.133 58.542 77.098 1.00 56.26 S ATOM 9064 SG CYS B 322 25.689 61.029 75.788 1.00 60.54 S Time building chain proxies: 3.33, per 1000 atoms: 0.23 Number of scatterers: 14540 At special positions: 0 Unit cell: (95.964, 130.86, 146.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 86 16.00 P 56 15.00 Mg 4 11.99 O 2806 8.00 N 2541 7.00 C 9043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 686.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 17 sheets defined 44.4% alpha, 19.1% beta 23 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.753A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 398 removed outlier: 5.642A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 481 through 501 removed outlier: 4.507A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 563 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.559A pdb=" N ASN A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.800A pdb=" N ALA A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 876 through 887 removed outlier: 4.714A pdb=" N ASN A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.656A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.764A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix removed outlier: 3.520A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.643A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 398 removed outlier: 5.644A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 481 through 501 removed outlier: 4.676A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 4.084A pdb=" N GLN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 748 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 762 removed outlier: 3.815A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 817 through 831 removed outlier: 4.684A pdb=" N HIS B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 879 through 887 removed outlier: 4.411A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 removed outlier: 6.514A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.520A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.520A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.551A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.301A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.333A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.244A pdb=" N THR A 776 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 895 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 778 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 24 removed outlier: 4.197A pdb=" N VAL B 18 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG B 62 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN B 20 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA B 64 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY B 22 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.489A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.489A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.355A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.157A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 776 through 779 removed outlier: 6.198A pdb=" N THR B 776 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE B 895 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG B 778 " --> pdb=" O ILE B 895 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2232 1.29 - 1.42: 4187 1.42 - 1.56: 8310 1.56 - 1.69: 107 1.69 - 1.82: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ALA A 64 " pdb=" C ALA A 64 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.23e-02 6.61e+03 3.51e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.30e-02 5.92e+03 3.29e+01 bond pdb=" CA MET A 63 " pdb=" C MET A 63 " ideal model delta sigma weight residual 1.522 1.456 0.067 1.20e-02 6.94e+03 3.08e+01 bond pdb=" CA ARG A 62 " pdb=" CB ARG A 62 " ideal model delta sigma weight residual 1.531 1.455 0.075 1.52e-02 4.33e+03 2.45e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.28e-02 6.10e+03 2.37e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 20041 2.06 - 4.12: 377 4.12 - 6.18: 39 6.18 - 8.24: 1 8.24 - 10.30: 5 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.14 100.84 10.30 1.08e+00 8.57e-01 9.09e+01 angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.28 119.58 -8.30 1.09e+00 8.42e-01 5.80e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" CB ASN B 638 " ideal model delta sigma weight residual 110.07 118.59 -8.52 1.45e+00 4.76e-01 3.45e+01 angle pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" C ARG B 134 " ideal model delta sigma weight residual 109.40 118.86 -9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" N LYS B 385 " pdb=" CA LYS B 385 " pdb=" C LYS B 385 " ideal model delta sigma weight residual 111.36 105.88 5.48 1.09e+00 8.42e-01 2.53e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.28: 8142 18.28 - 36.56: 713 36.56 - 54.84: 216 54.84 - 73.13: 110 73.13 - 91.41: 18 Dihedral angle restraints: 9199 sinusoidal: 4367 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 140.59 91.41 1 1.70e+01 3.46e-03 3.40e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO A 757 " pdb=" C PRO A 757 " pdb=" N THR A 758 " pdb=" CA THR A 758 " ideal model delta harmonic sigma weight residual 180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2037 0.071 - 0.143: 252 0.143 - 0.214: 7 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA LEU B 636 " pdb=" N LEU B 636 " pdb=" C LEU B 636 " pdb=" CB LEU B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP B 567 " pdb=" N ASP B 567 " pdb=" C ASP B 567 " pdb=" CB ASP B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 636 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU B 636 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU B 636 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 637 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 335 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C GLU A 335 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 335 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 336 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 694 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 695 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 695 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 695 " -0.031 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 75 2.49 - 3.09: 10190 3.09 - 3.70: 22409 3.70 - 4.30: 34876 4.30 - 4.90: 56098 Nonbonded interactions: 123648 Sorted by model distance: nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.888 2.170 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 1.953 3.060 nonbonded pdb=" O2' C T 3 " pdb=" OP1 A T 4 " model vdw 1.997 3.040 nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 2.044 3.060 nonbonded pdb=" OP2 A T 69 " pdb="MG MG T 104 " model vdw 2.047 2.170 ... (remaining 123643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.900 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14966 Z= 0.387 Angle : 0.707 10.297 20469 Z= 0.442 Chirality : 0.046 0.357 2298 Planarity : 0.006 0.067 2418 Dihedral : 16.918 91.407 6075 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.54 % Allowed : 11.84 % Favored : 87.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.14 % 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: 0.15 (0.20), residues: 1638 helix: 0.67 (0.20), residues: 638 sheet: 0.36 (0.31), residues: 274 loop : -0.40 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 778 TYR 0.017 0.002 TYR B 226 PHE 0.017 0.002 PHE A 223 TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.39 (14958) covalent geometry : angle 0.70658 / 0.44 (20463) hydrogen bonds : bond 0.12562 / 8.56 ( 646) hydrogen bonds : angle 5.57273 / 3.99 ( 1789) metal coordination : bond 0.00640 / 0.39 ( 8) metal coordination : angle 1.67084 / 3.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.567 Fit side-chains REVERT: A 134 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8746 (ptp-110) REVERT: A 262 LYS cc_start: 0.8353 (ptpp) cc_final: 0.7915 (mtmm) REVERT: A 657 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6636 (OUTLIER) REVERT: B 198 TYR cc_start: 0.6959 (p90) cc_final: 0.6733 (p90) outliers start: 8 outliers final: 3 residues processed: 199 average time/residue: 0.7640 time to fit residues: 164.4586 Evaluate side-chains 178 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 850 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 452 GLN A 633 ASN B 38 GLN B 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123664 restraints weight = 16549.335| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.86 r_work: 0.3166 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14966 Z= 0.145 Angle : 0.553 6.461 20469 Z= 0.300 Chirality : 0.042 0.154 2298 Planarity : 0.005 0.052 2418 Dihedral : 14.654 87.745 2707 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.83 % Allowed : 12.11 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1638 helix: 1.12 (0.20), residues: 646 sheet: 0.25 (0.30), residues: 268 loop : -0.17 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.020 0.002 TYR B 226 PHE 0.024 0.001 PHE B 800 TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14958) covalent geometry : angle 0.55183 / 0.30 (20463) hydrogen bonds : bond 0.05000 / 3.45 ( 646) hydrogen bonds : angle 4.69694 / 3.37 ( 1789) metal coordination : bond 0.00565 / 0.32 ( 8) metal coordination : angle 1.82681 / 3.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.553 Fit side-chains REVERT: A 262 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7828 (mtmm) REVERT: A 268 ASP cc_start: 0.7458 (p0) cc_final: 0.7045 (p0) REVERT: A 676 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 848 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7633 (m-70) REVERT: B 198 TYR cc_start: 0.6808 (p90) cc_final: 0.6602 (p90) REVERT: B 304 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7442 (ptpt) REVERT: B 690 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7048 (mpt-90) REVERT: B 720 ASP cc_start: 0.7224 (t0) cc_final: 0.6805 (m-30) REVERT: B 836 VAL cc_start: 0.3341 (OUTLIER) cc_final: 0.3131 (t) outliers start: 27 outliers final: 8 residues processed: 211 average time/residue: 0.6795 time to fit residues: 156.3891 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 690 ARG Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 479 GLN A 638 ASN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119996 restraints weight = 16766.751| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.90 r_work: 0.3099 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14966 Z= 0.186 Angle : 0.554 6.333 20469 Z= 0.296 Chirality : 0.043 0.142 2298 Planarity : 0.005 0.063 2418 Dihedral : 14.507 84.518 2702 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.23 % Allowed : 12.92 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.54 (0.20), residues: 1638 helix: 1.17 (0.20), residues: 646 sheet: 0.24 (0.30), residues: 268 loop : -0.23 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 291 TYR 0.012 0.002 TYR B 582 PHE 0.017 0.002 PHE B 800 TRP 0.012 0.002 TRP B 332 HIS 0.006 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (14958) covalent geometry : angle 0.55335 / 0.30 (20463) hydrogen bonds : bond 0.04805 / 3.34 ( 646) hydrogen bonds : angle 4.55052 / 3.26 ( 1789) metal coordination : bond 0.00488 / 0.31 ( 8) metal coordination : angle 1.12616 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.563 Fit side-chains REVERT: A 134 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8698 (ptp-110) REVERT: A 221 LYS cc_start: 0.7845 (tptp) cc_final: 0.7638 (tptp) REVERT: A 262 LYS cc_start: 0.8288 (ptpp) cc_final: 0.7795 (mtmm) REVERT: A 268 ASP cc_start: 0.7446 (p0) cc_final: 0.7058 (p0) REVERT: A 661 HIS cc_start: 0.6428 (p-80) cc_final: 0.6162 (p90) REVERT: A 676 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 848 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (m-70) REVERT: B 198 TYR cc_start: 0.6814 (p90) cc_final: 0.6592 (p90) REVERT: B 720 ASP cc_start: 0.7359 (t0) cc_final: 0.7042 (m-30) REVERT: B 836 VAL cc_start: 0.3197 (OUTLIER) cc_final: 0.2984 (t) outliers start: 33 outliers final: 9 residues processed: 208 average time/residue: 0.7017 time to fit residues: 158.7738 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 479 GLN A 742 GLN B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120174 restraints weight = 16762.264| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.89 r_work: 0.3101 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14966 Z= 0.187 Angle : 0.546 6.143 20469 Z= 0.292 Chirality : 0.043 0.176 2298 Planarity : 0.005 0.059 2418 Dihedral : 14.457 82.050 2702 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 13.33 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.51 (0.20), residues: 1638 helix: 1.18 (0.20), residues: 646 sheet: 0.16 (0.31), residues: 268 loop : -0.27 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 272 TYR 0.012 0.002 TYR B 582 PHE 0.012 0.001 PHE B 800 TRP 0.012 0.002 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (14958) covalent geometry : angle 0.54610 / 0.29 (20463) hydrogen bonds : bond 0.04658 / 3.24 ( 646) hydrogen bonds : angle 4.52464 / 3.24 ( 1789) metal coordination : bond 0.00539 / 0.34 ( 8) metal coordination : angle 0.89075 / 1.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.565 Fit side-chains REVERT: A 224 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7635 (mm-40) REVERT: A 268 ASP cc_start: 0.7371 (p0) cc_final: 0.6922 (p0) REVERT: A 676 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: A 689 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.7540 (ptm-80) REVERT: A 830 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.5932 (tpp) REVERT: A 848 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7618 (m-70) REVERT: B 118 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.6625 (p0) REVERT: B 198 TYR cc_start: 0.6758 (p90) cc_final: 0.6544 (p90) REVERT: B 720 ASP cc_start: 0.7397 (t0) cc_final: 0.7181 (m-30) REVERT: B 808 ASP cc_start: 0.8575 (m-30) cc_final: 0.8260 (m-30) REVERT: B 836 VAL cc_start: 0.3262 (OUTLIER) cc_final: 0.3047 (t) outliers start: 38 outliers final: 13 residues processed: 217 average time/residue: 0.7271 time to fit residues: 171.0364 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 HIS A 450 ASN A 479 GLN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122112 restraints weight = 16666.391| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3131 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14966 Z= 0.126 Angle : 0.504 7.811 20469 Z= 0.269 Chirality : 0.041 0.138 2298 Planarity : 0.004 0.044 2418 Dihedral : 14.395 78.517 2702 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.96 % Allowed : 14.61 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1638 helix: 1.37 (0.20), residues: 648 sheet: 0.27 (0.31), residues: 264 loop : -0.19 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 272 TYR 0.012 0.001 TYR A 740 PHE 0.011 0.001 PHE B 585 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14958) covalent geometry : angle 0.50373 / 0.27 (20463) hydrogen bonds : bond 0.04179 / 2.90 ( 646) hydrogen bonds : angle 4.40397 / 3.15 ( 1789) metal coordination : bond 0.00287 / 0.15 ( 8) metal coordination : angle 1.11506 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.584 Fit side-chains REVERT: A 224 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7572 (mm-40) REVERT: A 262 LYS cc_start: 0.8351 (ptpp) cc_final: 0.7796 (mtmm) REVERT: A 610 MET cc_start: 0.8825 (mtp) cc_final: 0.8596 (mtm) REVERT: A 657 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6528 (mt-10) REVERT: A 676 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 689 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7525 (ptm-80) REVERT: A 830 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5742 (tpp) REVERT: A 848 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7602 (m-70) REVERT: B 118 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.6633 (p0) REVERT: B 808 ASP cc_start: 0.8566 (m-30) cc_final: 0.8242 (m-30) REVERT: B 836 VAL cc_start: 0.3283 (OUTLIER) cc_final: 0.3062 (t) outliers start: 29 outliers final: 9 residues processed: 211 average time/residue: 0.6742 time to fit residues: 155.4122 Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 479 GLN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120649 restraints weight = 16744.069| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.91 r_work: 0.3098 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14966 Z= 0.205 Angle : 0.556 6.533 20469 Z= 0.294 Chirality : 0.043 0.161 2298 Planarity : 0.005 0.062 2418 Dihedral : 14.388 76.551 2702 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.50 % Allowed : 14.95 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.56 (0.20), residues: 1638 helix: 1.23 (0.20), residues: 648 sheet: 0.25 (0.31), residues: 264 loop : -0.28 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 272 TYR 0.016 0.002 TYR B 198 PHE 0.013 0.002 PHE A 320 TRP 0.013 0.002 TRP B 332 HIS 0.007 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (14958) covalent geometry : angle 0.55605 / 0.29 (20463) hydrogen bonds : bond 0.04647 / 3.24 ( 646) hydrogen bonds : angle 4.49774 / 3.22 ( 1789) metal coordination : bond 0.00837 / 0.51 ( 8) metal coordination : angle 0.92933 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.550 Fit side-chains REVERT: A 224 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: A 262 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7788 (mtmm) REVERT: A 268 ASP cc_start: 0.7423 (p0) cc_final: 0.7128 (p0) REVERT: A 290 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: A 610 MET cc_start: 0.8852 (mtp) cc_final: 0.8627 (mtm) REVERT: A 621 HIS cc_start: 0.7581 (m90) cc_final: 0.7201 (m90) REVERT: A 644 ASN cc_start: 0.7644 (m-40) cc_final: 0.7320 (p0) REVERT: A 657 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6668 (mt-10) REVERT: A 676 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 830 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5721 (tpp) REVERT: A 848 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7510 (m-70) REVERT: B 118 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.6703 (p0) REVERT: B 690 ARG cc_start: 0.7507 (mpt-90) cc_final: 0.7234 (mpt-90) REVERT: B 808 ASP cc_start: 0.8558 (m-30) cc_final: 0.8251 (m-30) outliers start: 37 outliers final: 14 residues processed: 208 average time/residue: 0.6681 time to fit residues: 151.9865 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120356 restraints weight = 16702.030| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.91 r_work: 0.3095 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14966 Z= 0.208 Angle : 0.568 8.161 20469 Z= 0.298 Chirality : 0.043 0.162 2298 Planarity : 0.005 0.060 2418 Dihedral : 14.394 75.310 2702 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.44 % Allowed : 15.16 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1638 helix: 1.15 (0.20), residues: 650 sheet: 0.24 (0.31), residues: 264 loop : -0.31 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 272 TYR 0.013 0.002 TYR B 582 PHE 0.015 0.002 PHE A 800 TRP 0.013 0.002 TRP B 332 HIS 0.007 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (14958) covalent geometry : angle 0.56803 / 0.30 (20463) hydrogen bonds : bond 0.04636 / 3.25 ( 646) hydrogen bonds : angle 4.51543 / 3.24 ( 1789) metal coordination : bond 0.00938 / 0.59 ( 8) metal coordination : angle 0.89296 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.662 Fit side-chains REVERT: A 224 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7581 (mm-40) REVERT: A 252 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7436 (t70) REVERT: A 262 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7799 (mtmm) REVERT: A 268 ASP cc_start: 0.7377 (p0) cc_final: 0.7124 (p0) REVERT: A 290 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: A 610 MET cc_start: 0.8861 (mtp) cc_final: 0.8593 (mtm) REVERT: A 621 HIS cc_start: 0.7598 (m90) cc_final: 0.7239 (m90) REVERT: A 644 ASN cc_start: 0.7609 (m-40) cc_final: 0.7284 (p0) REVERT: A 676 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 830 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5575 (tpp) REVERT: A 848 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7550 (m-70) REVERT: B 118 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.6771 (p0) REVERT: B 272 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7658 (mtm-85) REVERT: B 690 ARG cc_start: 0.7481 (mpt-90) cc_final: 0.7212 (mpt-90) REVERT: B 778 ARG cc_start: 0.6659 (mmt90) cc_final: 0.6218 (mmt-90) REVERT: B 808 ASP cc_start: 0.8565 (m-30) cc_final: 0.8259 (m-30) REVERT: B 836 VAL cc_start: 0.3217 (OUTLIER) cc_final: 0.2979 (t) outliers start: 36 outliers final: 17 residues processed: 208 average time/residue: 0.6661 time to fit residues: 151.1614 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122737 restraints weight = 16662.398| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.84 r_work: 0.3138 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14966 Z= 0.119 Angle : 0.506 7.502 20469 Z= 0.269 Chirality : 0.041 0.182 2298 Planarity : 0.004 0.038 2418 Dihedral : 14.329 73.852 2702 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 16.04 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.82 (0.21), residues: 1638 helix: 1.48 (0.20), residues: 648 sheet: 0.28 (0.31), residues: 264 loop : -0.13 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 272 TYR 0.011 0.001 TYR A 740 PHE 0.022 0.001 PHE A 800 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14958) covalent geometry : angle 0.50583 / 0.27 (20463) hydrogen bonds : bond 0.03991 / 2.77 ( 646) hydrogen bonds : angle 4.34561 / 3.12 ( 1789) metal coordination : bond 0.00479 / 0.26 ( 8) metal coordination : angle 1.05775 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.518 Fit side-chains REVERT: A 221 LYS cc_start: 0.8005 (ptpt) cc_final: 0.7705 (ptpp) REVERT: A 224 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7569 (mm-40) REVERT: A 262 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7837 (mtmm) REVERT: A 268 ASP cc_start: 0.7355 (p0) cc_final: 0.7136 (p0) REVERT: A 290 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: A 644 ASN cc_start: 0.7547 (m-40) cc_final: 0.7273 (p0) REVERT: A 657 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6613 (mt-10) REVERT: A 661 HIS cc_start: 0.6439 (p-80) cc_final: 0.6096 (p-80) REVERT: A 676 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 830 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6126 (mtp) REVERT: A 848 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7510 (m-70) REVERT: B 118 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.6776 (p0) REVERT: B 626 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.5135 (mmm160) REVERT: B 778 ARG cc_start: 0.6616 (mmt90) cc_final: 0.6137 (mmt-90) REVERT: B 836 VAL cc_start: 0.2983 (OUTLIER) cc_final: 0.2765 (t) outliers start: 26 outliers final: 8 residues processed: 205 average time/residue: 0.5821 time to fit residues: 130.6610 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 626 ARG Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 46 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121821 restraints weight = 16764.830| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.91 r_work: 0.3104 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14966 Z= 0.178 Angle : 0.558 9.727 20469 Z= 0.291 Chirality : 0.042 0.223 2298 Planarity : 0.004 0.056 2418 Dihedral : 14.320 74.146 2702 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.89 % Allowed : 16.31 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.72 (0.21), residues: 1638 helix: 1.35 (0.20), residues: 650 sheet: 0.29 (0.31), residues: 264 loop : -0.16 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 272 TYR 0.013 0.002 TYR A 740 PHE 0.021 0.001 PHE A 800 TRP 0.011 0.002 TRP B 332 HIS 0.007 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (14958) covalent geometry : angle 0.55775 / 0.29 (20463) hydrogen bonds : bond 0.04368 / 3.05 ( 646) hydrogen bonds : angle 4.42677 / 3.18 ( 1789) metal coordination : bond 0.00597 / 0.38 ( 8) metal coordination : angle 0.79021 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.635 Fit side-chains REVERT: A 221 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7775 (ptpp) REVERT: A 224 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: A 262 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7844 (mtmm) REVERT: A 268 ASP cc_start: 0.7337 (p0) cc_final: 0.7134 (p0) REVERT: A 290 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: A 429 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8194 (ttpt) REVERT: A 644 ASN cc_start: 0.7559 (m-40) cc_final: 0.7299 (p0) REVERT: A 657 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6613 (mt-10) REVERT: A 661 HIS cc_start: 0.6473 (p-80) cc_final: 0.6159 (p-80) REVERT: A 676 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 848 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: B 118 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.6811 (p0) REVERT: B 272 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7661 (mtm-85) REVERT: B 626 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5221 (mmm160) REVERT: B 690 ARG cc_start: 0.7562 (mpt-90) cc_final: 0.7262 (mpt-90) REVERT: B 778 ARG cc_start: 0.6661 (mmt90) cc_final: 0.6199 (mmt-90) REVERT: B 836 VAL cc_start: 0.2940 (OUTLIER) cc_final: 0.2721 (t) outliers start: 28 outliers final: 13 residues processed: 197 average time/residue: 0.6266 time to fit residues: 135.0856 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 626 ARG Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123486 restraints weight = 16636.834| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.86 r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14966 Z= 0.115 Angle : 0.522 9.913 20469 Z= 0.273 Chirality : 0.040 0.187 2298 Planarity : 0.004 0.051 2418 Dihedral : 14.287 73.868 2702 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 16.85 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.88 (0.21), residues: 1638 helix: 1.50 (0.20), residues: 650 sheet: 0.30 (0.31), residues: 264 loop : -0.05 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 272 TYR 0.012 0.001 TYR A 740 PHE 0.028 0.001 PHE A 800 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (14958) covalent geometry : angle 0.52210 / 0.27 (20463) hydrogen bonds : bond 0.03930 / 2.72 ( 646) hydrogen bonds : angle 4.34599 / 3.15 ( 1789) metal coordination : bond 0.00433 / 0.24 ( 8) metal coordination : angle 1.00253 / 2.05 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.520 Fit side-chains REVERT: A 221 LYS cc_start: 0.7984 (ptpt) cc_final: 0.7680 (ptpp) REVERT: A 224 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7572 (mm-40) REVERT: A 262 LYS cc_start: 0.8339 (ptpp) cc_final: 0.7882 (mtmm) REVERT: A 268 ASP cc_start: 0.7325 (p0) cc_final: 0.7121 (p0) REVERT: A 290 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: A 644 ASN cc_start: 0.7540 (m-40) cc_final: 0.7303 (p0) REVERT: A 657 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6615 (mt-10) REVERT: A 661 HIS cc_start: 0.6444 (p-80) cc_final: 0.6195 (p-80) REVERT: A 676 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 848 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: B 118 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.6763 (p0) REVERT: B 272 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7672 (mtm-85) REVERT: B 626 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.5073 (mmm160) REVERT: B 690 ARG cc_start: 0.7556 (mpt-90) cc_final: 0.7272 (mpt-90) REVERT: B 778 ARG cc_start: 0.6591 (mmt90) cc_final: 0.6138 (mmt-90) REVERT: B 836 VAL cc_start: 0.2865 (OUTLIER) cc_final: 0.2650 (t) outliers start: 20 outliers final: 8 residues processed: 200 average time/residue: 0.6031 time to fit residues: 131.7664 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 626 ARG Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123955 restraints weight = 16703.226| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14966 Z= 0.125 Angle : 0.529 11.424 20469 Z= 0.275 Chirality : 0.041 0.183 2298 Planarity : 0.004 0.047 2418 Dihedral : 14.260 73.866 2702 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 16.64 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.90 (0.21), residues: 1638 helix: 1.51 (0.20), residues: 650 sheet: 0.28 (0.31), residues: 274 loop : -0.02 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 272 TYR 0.013 0.001 TYR A 740 PHE 0.031 0.001 PHE A 800 TRP 0.009 0.001 TRP B 413 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14958) covalent geometry : angle 0.52912 / 0.28 (20463) hydrogen bonds : bond 0.03961 / 2.74 ( 646) hydrogen bonds : angle 4.32875 / 3.14 ( 1789) metal coordination : bond 0.00248 / 0.13 ( 8) metal coordination : angle 0.86428 / 1.66 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5849.63 seconds wall clock time: 100 minutes 33.85 seconds (6033.85 seconds total)