Starting phenix.real_space_refine on Thu Aug 6 08:37:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmx_51457/08_2026/9gmx_51457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmx_51457/08_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_51457/08_2026/9gmx_51457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmx_51457/08_2026/9gmx_51457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gmx_51457/08_2026/9gmx_51457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmx_51457/08_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-2.2rc3-6140/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, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 2.91, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 526.8 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: 1.66 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: 2.97 Time building geometry restraints manager: 1.42 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: 19971 2.06 - 4.12: 447 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: 1982 0.071 - 0.143: 307 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 2.320 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 2.320 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: 5.630 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.720 Find NCS groups from input model: 0.210 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- 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= 0.394 Angle : 0.728 10.297 20469 Z= 0.469 Chirality : 0.048 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 0.00727 / 0.39 (14958) covalent geometry : angle 0.72766 / 0.47 (20463) hydrogen bonds : bond 0.12562 / 8.95 ( 646) hydrogen bonds : angle 5.57273 / 4.01 ( 1789) metal coordination : bond 0.00640 / 0.65 ( 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 : 0.534 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: 0.6741 time to fit residues: 145.4779 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 : 0.500 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.162176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123717 restraints weight = 16627.046| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.84 r_work: 0.3170 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14966 Z= 0.142 Angle : 0.558 6.588 20469 Z= 0.302 Chirality : 0.042 0.153 2298 Planarity : 0.005 0.054 2418 Dihedral : 14.612 87.937 2707 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.83 % Allowed : 11.98 % Favored : 86.20 % 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: 1.13 (0.20), residues: 646 sheet: 0.25 (0.30), residues: 268 loop : -0.16 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.021 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 B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14958) covalent geometry : angle 0.55728 / 0.30 (20463) hydrogen bonds : bond 0.04948 / 3.50 ( 646) hydrogen bonds : angle 4.68958 / 3.39 ( 1789) metal coordination : bond 0.00588 / 0.52 ( 8) metal coordination : angle 1.84416 / 3.60 ( 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 : 0.564 Fit side-chains REVERT: A 262 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7838 (mtmm) REVERT: A 268 ASP cc_start: 0.7443 (p0) cc_final: 0.7035 (p0) REVERT: A 676 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: A 848 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7647 (m-70) REVERT: B 198 TYR cc_start: 0.6770 (p90) cc_final: 0.6569 (p90) REVERT: B 304 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7454 (ptpt) REVERT: B 690 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7053 (mpt-90) REVERT: B 720 ASP cc_start: 0.7236 (t0) cc_final: 0.6810 (m-30) REVERT: B 836 VAL cc_start: 0.3320 (OUTLIER) cc_final: 0.3109 (t) outliers start: 27 outliers final: 8 residues processed: 211 average time/residue: 0.6641 time to fit residues: 152.8623 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.9990 chunk 113 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN A 661 HIS 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 = 0.3840 r_free = 0.3840 target = 0.160170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120267 restraints weight = 16794.119| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.91 r_work: 0.3105 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14966 Z= 0.167 Angle : 0.546 7.640 20469 Z= 0.291 Chirality : 0.042 0.141 2298 Planarity : 0.005 0.060 2418 Dihedral : 14.466 84.405 2702 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.23 % Allowed : 12.72 % Favored : 85.05 % 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: 0.61 (0.20), residues: 1638 helix: 1.22 (0.20), residues: 646 sheet: 0.24 (0.30), residues: 268 loop : -0.18 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 291 TYR 0.011 0.002 TYR B 582 PHE 0.017 0.001 PHE B 800 TRP 0.012 0.002 TRP B 332 HIS 0.006 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (14958) covalent geometry : angle 0.54528 / 0.29 (20463) hydrogen bonds : bond 0.04751 / 3.37 ( 646) hydrogen bonds : angle 4.53908 / 3.28 ( 1789) metal coordination : bond 0.00286 / 0.37 ( 8) metal coordination : angle 1.28122 / 2.68 ( 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 : 0.551 Fit side-chains REVERT: A 221 LYS cc_start: 0.7823 (tptp) cc_final: 0.7594 (tptp) REVERT: A 262 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7800 (mtmm) REVERT: A 268 ASP cc_start: 0.7442 (p0) cc_final: 0.7044 (p0) REVERT: A 661 HIS cc_start: 0.6403 (p-80) cc_final: 0.6130 (p90) REVERT: A 676 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 848 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7603 (m-70) REVERT: B 146 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: B 198 TYR cc_start: 0.6796 (p90) cc_final: 0.6578 (p90) REVERT: B 720 ASP cc_start: 0.7328 (t0) cc_final: 0.7005 (m-30) REVERT: B 836 VAL cc_start: 0.3187 (OUTLIER) cc_final: 0.2976 (t) outliers start: 33 outliers final: 11 residues processed: 208 average time/residue: 0.6731 time to fit residues: 152.1310 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 146 ARG 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: 0.9990 chunk 3 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN A 638 ASN 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 = 0.3801 r_free = 0.3801 target = 0.156784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117731 restraints weight = 16837.743| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.90 r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 14966 Z= 0.337 Angle : 0.675 6.450 20469 Z= 0.354 Chirality : 0.049 0.156 2298 Planarity : 0.006 0.078 2418 Dihedral : 14.541 83.531 2702 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.11 % Allowed : 13.53 % Favored : 83.36 % 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: 0.10 (0.20), residues: 1638 helix: 0.72 (0.20), residues: 648 sheet: 0.21 (0.31), residues: 264 loop : -0.49 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 626 TYR 0.021 0.002 TYR B 804 PHE 0.017 0.002 PHE A 320 TRP 0.019 0.003 TRP B 332 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.34 (14958) covalent geometry : angle 0.67498 / 0.35 (20463) hydrogen bonds : bond 0.05671 / 4.09 ( 646) hydrogen bonds : angle 4.79383 / 3.46 ( 1789) metal coordination : bond 0.02119 / 2.40 ( 8) metal coordination : angle 1.13699 / 1.43 ( 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 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 0.561 Fit side-chains REVERT: A 224 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7695 (mm-40) REVERT: A 268 ASP cc_start: 0.7404 (p0) cc_final: 0.6955 (p0) REVERT: A 661 HIS cc_start: 0.6466 (p-80) cc_final: 0.6244 (p90) REVERT: A 676 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 830 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.5938 (tpp) REVERT: A 848 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7657 (m-70) REVERT: B 118 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.6780 (p0) REVERT: B 146 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: B 626 ARG cc_start: 0.5941 (mmm-85) cc_final: 0.5625 (mmm160) REVERT: B 720 ASP cc_start: 0.7364 (t0) cc_final: 0.7146 (m-30) REVERT: B 724 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: B 836 VAL cc_start: 0.3329 (OUTLIER) cc_final: 0.3103 (t) REVERT: B 849 ILE cc_start: 0.7911 (mt) cc_final: 0.7688 (mt) outliers start: 46 outliers final: 21 residues processed: 216 average time/residue: 0.7048 time to fit residues: 165.2744 Evaluate side-chains 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 230 THR 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 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 724 ARG Chi-restraints excluded: chain B residue 761 LEU 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: 0.6980 chunk 135 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 38 GLN B 99 GLN B 638 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.160840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121363 restraints weight = 16675.976| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.88 r_work: 0.3122 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1564 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= 0.128 Angle : 0.524 7.655 20469 Z= 0.281 Chirality : 0.041 0.137 2298 Planarity : 0.004 0.041 2418 Dihedral : 14.403 80.763 2702 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.23 % Allowed : 14.82 % Favored : 82.95 % 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: 0.52 (0.20), residues: 1638 helix: 1.18 (0.20), residues: 648 sheet: 0.19 (0.31), residues: 264 loop : -0.27 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 778 TYR 0.012 0.001 TYR A 582 PHE 0.011 0.001 PHE B 585 TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14958) covalent geometry : angle 0.52390 / 0.28 (20463) hydrogen bonds : bond 0.04330 / 3.06 ( 646) hydrogen bonds : angle 4.51894 / 3.26 ( 1789) metal coordination : bond 0.00371 / 0.25 ( 8) metal coordination : angle 1.09513 / 2.17 ( 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 228 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7559 (mm-40) REVERT: A 262 LYS cc_start: 0.8343 (ptpp) cc_final: 0.7806 (mtmm) REVERT: A 657 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6656 (mt-10) REVERT: A 661 HIS cc_start: 0.6478 (p-80) cc_final: 0.6265 (p90) REVERT: A 676 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 830 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.5729 (tpp) REVERT: A 848 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7562 (m-70) REVERT: A 885 LEU cc_start: 0.8448 (tp) cc_final: 0.8247 (tm) REVERT: B 118 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6742 (p0) REVERT: B 778 ARG cc_start: 0.6696 (mmt90) cc_final: 0.6176 (mmt-90) REVERT: B 808 ASP cc_start: 0.8566 (m-30) cc_final: 0.8236 (m-30) REVERT: B 836 VAL cc_start: 0.3309 (OUTLIER) cc_final: 0.3091 (t) outliers start: 33 outliers final: 12 residues processed: 216 average time/residue: 0.6747 time to fit residues: 158.4124 Evaluate side-chains 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 227 VAL 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 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 426 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 788 ILE 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: 3.9990 chunk 38 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN 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 = 0.3828 r_free = 0.3828 target = 0.159199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120059 restraints weight = 16770.542| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.93 r_work: 0.3090 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14966 Z= 0.205 Angle : 0.568 6.427 20469 Z= 0.299 Chirality : 0.043 0.140 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.388 77.970 2702 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.64 % Allowed : 15.43 % 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: 0.47 (0.20), residues: 1638 helix: 1.11 (0.20), residues: 648 sheet: 0.19 (0.31), residues: 264 loop : -0.28 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 272 TYR 0.014 0.002 TYR B 582 PHE 0.013 0.002 PHE A 320 TRP 0.013 0.002 TRP B 332 HIS 0.004 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (14958) covalent geometry : angle 0.56819 / 0.30 (20463) hydrogen bonds : bond 0.04757 / 3.39 ( 646) hydrogen bonds : angle 4.53524 / 3.27 ( 1789) metal coordination : bond 0.00803 / 0.97 ( 8) metal coordination : angle 0.95658 / 1.55 ( 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 228 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7604 (mm-40) REVERT: A 268 ASP cc_start: 0.7427 (p0) cc_final: 0.7134 (p0) REVERT: A 290 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: A 661 HIS cc_start: 0.6503 (p-80) cc_final: 0.6255 (p-80) REVERT: A 676 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 830 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5639 (tpp) REVERT: A 848 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7546 (m-70) REVERT: B 118 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.6802 (p0) REVERT: B 808 ASP cc_start: 0.8558 (m-30) cc_final: 0.8264 (m-30) outliers start: 39 outliers final: 17 residues processed: 211 average time/residue: 0.6181 time to fit residues: 142.3215 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 400 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 192 LEU Chi-restraints excluded: chain B residue 197 ASP 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 788 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 850 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: 10.0000 chunk 98 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119788 restraints weight = 16756.490| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.88 r_work: 0.3084 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14966 Z= 0.215 Angle : 0.578 7.693 20469 Z= 0.303 Chirality : 0.044 0.188 2298 Planarity : 0.005 0.062 2418 Dihedral : 14.382 76.447 2702 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 15.76 % 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: 0.41 (0.20), residues: 1638 helix: 1.07 (0.20), residues: 648 sheet: 0.18 (0.31), residues: 264 loop : -0.32 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 272 TYR 0.013 0.002 TYR B 582 PHE 0.012 0.002 PHE A 320 TRP 0.013 0.002 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (14958) covalent geometry : angle 0.57759 / 0.30 (20463) hydrogen bonds : bond 0.04763 / 3.41 ( 646) hydrogen bonds : angle 4.56078 / 3.29 ( 1789) metal coordination : bond 0.00964 / 1.18 ( 8) metal coordination : angle 0.89745 / 1.22 ( 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 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.435 Fit side-chains REVERT: A 224 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7603 (mm-40) REVERT: A 268 ASP cc_start: 0.7364 (p0) cc_final: 0.7120 (p0) REVERT: A 290 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: A 661 HIS cc_start: 0.6470 (p-80) cc_final: 0.6212 (p-80) REVERT: A 676 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 848 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7543 (m-70) REVERT: B 118 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.6821 (p0) REVERT: B 146 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8061 (mtm180) REVERT: B 272 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7679 (mtm-85) REVERT: B 778 ARG cc_start: 0.6690 (mmt90) cc_final: 0.6254 (mmt-90) REVERT: B 808 ASP cc_start: 0.8559 (m-30) cc_final: 0.8264 (m-30) REVERT: B 836 VAL cc_start: 0.3276 (OUTLIER) cc_final: 0.3046 (t) outliers start: 34 outliers final: 22 residues processed: 212 average time/residue: 0.6089 time to fit residues: 141.0824 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 227 VAL 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 429 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE 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 146 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP 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 761 LEU 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 850 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: 2.9990 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122690 restraints weight = 16719.215| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.88 r_work: 0.3129 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14966 Z= 0.123 Angle : 0.523 8.186 20469 Z= 0.277 Chirality : 0.041 0.180 2298 Planarity : 0.004 0.042 2418 Dihedral : 14.298 73.973 2702 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.69 % Allowed : 16.78 % Favored : 81.53 % 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: 0.67 (0.21), residues: 1638 helix: 1.32 (0.20), residues: 650 sheet: 0.23 (0.31), residues: 264 loop : -0.19 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 778 TYR 0.012 0.001 TYR A 740 PHE 0.016 0.001 PHE A 800 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14958) covalent geometry : angle 0.52295 / 0.28 (20463) hydrogen bonds : bond 0.04135 / 2.92 ( 646) hydrogen bonds : angle 4.42031 / 3.19 ( 1789) metal coordination : bond 0.00333 / 0.22 ( 8) metal coordination : angle 0.97811 / 1.97 ( 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: 25 poor density : 189 time to evaluate : 0.541 Fit side-chains REVERT: A 224 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7566 (mm-40) REVERT: A 268 ASP cc_start: 0.7354 (p0) cc_final: 0.7143 (p0) REVERT: A 290 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: A 657 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6767 (mt-10) REVERT: A 676 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 848 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7540 (m-70) REVERT: B 118 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.6840 (p0) REVERT: B 690 ARG cc_start: 0.7493 (mpt-90) cc_final: 0.7219 (mpt-90) REVERT: B 778 ARG cc_start: 0.6621 (mmt90) cc_final: 0.6159 (mmt-90) REVERT: B 808 ASP cc_start: 0.8539 (m-30) cc_final: 0.8252 (m-30) REVERT: B 836 VAL cc_start: 0.3028 (OUTLIER) cc_final: 0.2808 (t) outliers start: 25 outliers final: 12 residues processed: 205 average time/residue: 0.6395 time to fit residues: 142.8813 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 227 VAL 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 43 LYS 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 788 ILE Chi-restraints excluded: chain B residue 836 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: 9.9990 chunk 152 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 46 optimal weight: 0.0170 overall best weight: 2.5624 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.158546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119205 restraints weight = 16902.150| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.94 r_work: 0.3059 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 14966 Z= 0.256 Angle : 0.614 8.227 20469 Z= 0.320 Chirality : 0.045 0.228 2298 Planarity : 0.005 0.066 2418 Dihedral : 14.362 74.430 2702 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.10 % Allowed : 16.58 % Favored : 81.33 % 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: 0.39 (0.20), residues: 1638 helix: 1.03 (0.20), residues: 650 sheet: 0.24 (0.31), residues: 264 loop : -0.35 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 272 TYR 0.016 0.002 TYR B 309 PHE 0.017 0.002 PHE A 800 TRP 0.015 0.002 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (14958) covalent geometry : angle 0.61377 / 0.32 (20463) hydrogen bonds : bond 0.04946 / 3.56 ( 646) hydrogen bonds : angle 4.59242 / 3.31 ( 1789) metal coordination : bond 0.01362 / 1.65 ( 8) metal coordination : angle 1.08268 / 1.23 ( 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 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.537 Fit side-chains REVERT: A 224 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7621 (mm-40) REVERT: A 268 ASP cc_start: 0.7363 (p0) cc_final: 0.7155 (p0) REVERT: A 290 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: A 644 ASN cc_start: 0.7632 (m-40) cc_final: 0.7292 (p0) REVERT: A 676 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 848 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7556 (m-70) REVERT: B 118 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.6815 (p0) REVERT: B 146 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7640 (mtm110) REVERT: B 272 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7675 (mtm-85) REVERT: B 778 ARG cc_start: 0.6680 (mmt90) cc_final: 0.6196 (mmt-90) REVERT: B 808 ASP cc_start: 0.8568 (m-30) cc_final: 0.8279 (m-30) REVERT: B 836 VAL cc_start: 0.3080 (OUTLIER) cc_final: 0.2860 (t) outliers start: 31 outliers final: 17 residues processed: 206 average time/residue: 0.6581 time to fit residues: 147.8115 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 VAL 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 146 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP 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 788 ILE 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: 0.9980 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 157 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121940 restraints weight = 16709.871| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.86 r_work: 0.3136 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14966 Z= 0.120 Angle : 0.531 8.555 20469 Z= 0.280 Chirality : 0.041 0.240 2298 Planarity : 0.004 0.052 2418 Dihedral : 14.273 73.963 2702 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 17.46 % Favored : 81.12 % 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: 0.67 (0.21), residues: 1638 helix: 1.31 (0.20), residues: 650 sheet: 0.24 (0.31), residues: 264 loop : -0.18 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 272 TYR 0.013 0.001 TYR A 740 PHE 0.024 0.001 PHE A 800 TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14958) covalent geometry : angle 0.53075 / 0.28 (20463) hydrogen bonds : bond 0.04096 / 2.90 ( 646) hydrogen bonds : angle 4.43391 / 3.20 ( 1789) metal coordination : bond 0.00308 / 0.21 ( 8) metal coordination : angle 0.94251 / 1.87 ( 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 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.533 Fit side-chains REVERT: A 224 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7538 (mm-40) REVERT: A 268 ASP cc_start: 0.7333 (p0) cc_final: 0.7127 (p0) REVERT: A 290 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: A 644 ASN cc_start: 0.7591 (m-40) cc_final: 0.7294 (p0) REVERT: A 657 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6675 (mt-10) REVERT: A 676 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 848 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7556 (m-70) REVERT: B 118 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.6818 (p0) REVERT: B 146 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7907 (mtm180) REVERT: B 272 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7666 (mtm-85) REVERT: B 778 ARG cc_start: 0.6585 (mmt90) cc_final: 0.6126 (mmt-90) REVERT: B 836 VAL cc_start: 0.2929 (OUTLIER) cc_final: 0.2713 (t) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.6372 time to fit residues: 139.7152 Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 397 LEU 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 146 ARG 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 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 788 ILE 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: 0.9980 chunk 46 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 157 optimal weight: 0.0060 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.162920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123994 restraints weight = 16773.867| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.87 r_work: 0.3160 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14966 Z= 0.115 Angle : 0.516 8.728 20469 Z= 0.272 Chirality : 0.040 0.182 2298 Planarity : 0.004 0.050 2418 Dihedral : 14.194 73.971 2702 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 17.73 % Favored : 80.85 % 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: 0.91 (0.21), residues: 1638 helix: 1.48 (0.20), residues: 650 sheet: 0.33 (0.31), residues: 284 loop : -0.01 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 272 TYR 0.014 0.001 TYR A 740 PHE 0.026 0.001 PHE A 800 TRP 0.010 0.001 TRP B 413 HIS 0.003 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14958) covalent geometry : angle 0.51592 / 0.27 (20463) hydrogen bonds : bond 0.03931 / 2.75 ( 646) hydrogen bonds : angle 4.32350 / 3.14 ( 1789) metal coordination : bond 0.00519 / 0.37 ( 8) metal coordination : angle 1.02709 / 2.05 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5713.37 seconds wall clock time: 98 minutes 5.74 seconds (5885.74 seconds total)