Starting phenix.real_space_refine on Tue Dec 31 01:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_51457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_51457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_51457.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_51457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmx_51457/12_2024/9gmx_51457.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.90, per 1000 atoms: 0.68 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: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 6.23 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: 6.59 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2232 1.29 - 1.42: 4187 1.42 - 1.56: 8310 1.56 - 1.69: 107 1.69 - 1.82: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ALA A 64 " pdb=" C ALA A 64 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.23e-02 6.61e+03 3.51e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.30e-02 5.92e+03 3.29e+01 bond pdb=" CA MET A 63 " pdb=" C MET A 63 " ideal model delta sigma weight residual 1.522 1.456 0.067 1.20e-02 6.94e+03 3.08e+01 bond pdb=" CA ARG A 62 " pdb=" CB ARG A 62 " ideal model delta sigma weight residual 1.531 1.455 0.075 1.52e-02 4.33e+03 2.45e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.28e-02 6.10e+03 2.37e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 20041 2.06 - 4.12: 377 4.12 - 6.18: 39 6.18 - 8.24: 1 8.24 - 10.30: 5 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.14 100.84 10.30 1.08e+00 8.57e-01 9.09e+01 angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.28 119.58 -8.30 1.09e+00 8.42e-01 5.80e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" CB ASN B 638 " ideal model delta sigma weight residual 110.07 118.59 -8.52 1.45e+00 4.76e-01 3.45e+01 angle pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" C ARG B 134 " ideal model delta sigma weight residual 109.40 118.86 -9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" N LYS B 385 " pdb=" CA LYS B 385 " pdb=" C LYS B 385 " ideal model delta sigma weight residual 111.36 105.88 5.48 1.09e+00 8.42e-01 2.53e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.28: 8142 18.28 - 36.56: 713 36.56 - 54.84: 216 54.84 - 73.13: 110 73.13 - 91.41: 18 Dihedral angle restraints: 9199 sinusoidal: 4367 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 140.59 91.41 1 1.70e+01 3.46e-03 3.40e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO A 757 " pdb=" C PRO A 757 " pdb=" N THR A 758 " pdb=" CA THR A 758 " ideal model delta harmonic sigma weight residual 180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2037 0.071 - 0.143: 252 0.143 - 0.214: 7 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA LEU B 636 " pdb=" N LEU B 636 " pdb=" C LEU B 636 " pdb=" CB LEU B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP B 567 " pdb=" N ASP B 567 " pdb=" C ASP B 567 " pdb=" CB ASP B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 636 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU B 636 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU B 636 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 637 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 335 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C GLU A 335 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 335 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 336 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 694 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 695 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 695 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 695 " -0.031 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 75 2.49 - 3.09: 10190 3.09 - 3.70: 22409 3.70 - 4.30: 34876 4.30 - 4.90: 56098 Nonbonded interactions: 123648 Sorted by model distance: nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.888 2.170 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 1.953 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 44.930 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 14958 Z= 0.470 Angle : 0.707 10.297 20463 Z= 0.402 Chirality : 0.046 0.357 2298 Planarity : 0.006 0.067 2418 Dihedral : 16.918 91.407 6075 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.54 % Allowed : 11.84 % Favored : 87.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 420 PHE 0.017 0.002 PHE A 223 TYR 0.017 0.002 TYR B 226 ARG 0.008 0.001 ARG B 778 *********************** 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 : 1.627 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: 1.7004 time to fit residues: 366.6017 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 : 1.765 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 452 GLN A 633 ASN B 38 GLN B 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14958 Z= 0.183 Angle : 0.538 8.237 20463 Z= 0.284 Chirality : 0.041 0.151 2298 Planarity : 0.004 0.055 2418 Dihedral : 14.559 92.736 2707 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.69 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1638 helix: 1.27 (0.20), residues: 646 sheet: 0.26 (0.30), residues: 268 loop : -0.10 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.006 0.001 HIS B 625 PHE 0.028 0.001 PHE B 800 TYR 0.018 0.001 TYR B 226 ARG 0.008 0.001 ARG B 617 *********************** 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 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.693 Fit side-chains REVERT: A 221 LYS cc_start: 0.7709 (tptp) cc_final: 0.7412 (tptp) REVERT: A 268 ASP cc_start: 0.7316 (p0) cc_final: 0.6927 (p0) REVERT: A 610 MET cc_start: 0.8552 (mtp) cc_final: 0.8334 (mtm) REVERT: A 657 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6736 (OUTLIER) REVERT: A 661 HIS cc_start: 0.6242 (p-80) cc_final: 0.5968 (p90) REVERT: A 848 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.7023 (m-70) REVERT: B 720 ASP cc_start: 0.7133 (t0) cc_final: 0.6839 (m-30) REVERT: B 836 VAL cc_start: 0.3098 (OUTLIER) cc_final: 0.2884 (t) outliers start: 25 outliers final: 10 residues processed: 216 average time/residue: 1.5017 time to fit residues: 353.5412 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 0.0980 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 479 GLN A 742 GLN B 38 GLN B 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14958 Z= 0.281 Angle : 0.562 8.540 20463 Z= 0.290 Chirality : 0.042 0.143 2298 Planarity : 0.005 0.065 2418 Dihedral : 14.435 89.631 2702 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1638 helix: 1.28 (0.20), residues: 646 sheet: 0.30 (0.31), residues: 268 loop : -0.22 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 332 HIS 0.005 0.001 HIS B 848 PHE 0.016 0.001 PHE B 800 TYR 0.015 0.002 TYR B 198 ARG 0.010 0.001 ARG B 291 *********************** 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 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 1.695 Fit side-chains REVERT: A 224 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7385 (mm-40) REVERT: A 268 ASP cc_start: 0.7275 (p0) cc_final: 0.6904 (p0) REVERT: A 610 MET cc_start: 0.8590 (mtp) cc_final: 0.8369 (mtm) REVERT: A 657 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6859 (OUTLIER) REVERT: A 661 HIS cc_start: 0.6238 (p-80) cc_final: 0.5978 (p90) REVERT: A 676 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: A 848 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.7050 (m-70) REVERT: B 724 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7441 (mtm180) REVERT: B 788 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6324 (mp) REVERT: B 808 ASP cc_start: 0.8411 (m-30) cc_final: 0.7976 (m-30) REVERT: B 836 VAL cc_start: 0.3064 (OUTLIER) cc_final: 0.2847 (t) outliers start: 33 outliers final: 11 residues processed: 211 average time/residue: 1.5236 time to fit residues: 349.4999 Evaluate side-chains 196 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 300 VAL 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 724 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14958 Z= 0.225 Angle : 0.527 8.447 20463 Z= 0.273 Chirality : 0.041 0.137 2298 Planarity : 0.004 0.052 2418 Dihedral : 14.373 88.246 2702 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.03 % Allowed : 14.21 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1638 helix: 1.37 (0.20), residues: 648 sheet: 0.25 (0.31), residues: 268 loop : -0.20 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 PHE 0.013 0.001 PHE B 800 TYR 0.012 0.001 TYR A 740 ARG 0.007 0.000 ARG B 272 *********************** 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 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.632 Fit side-chains REVERT: A 224 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7389 (mm-40) REVERT: A 262 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7836 (mtmm) REVERT: A 610 MET cc_start: 0.8578 (mtp) cc_final: 0.8316 (mtm) REVERT: A 644 ASN cc_start: 0.7595 (m-40) cc_final: 0.7344 (p0) REVERT: A 657 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6960 (OUTLIER) REVERT: A 676 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: A 830 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.5814 (tpp) REVERT: A 848 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.7047 (m-70) REVERT: B 808 ASP cc_start: 0.8357 (m-30) cc_final: 0.7948 (m-30) outliers start: 30 outliers final: 14 residues processed: 212 average time/residue: 1.4920 time to fit residues: 343.9523 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 192 LEU 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 600 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 479 GLN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14958 Z= 0.259 Angle : 0.546 8.362 20463 Z= 0.281 Chirality : 0.042 0.163 2298 Planarity : 0.004 0.059 2418 Dihedral : 14.354 86.824 2702 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.23 % Allowed : 14.95 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1638 helix: 1.35 (0.20), residues: 648 sheet: 0.18 (0.31), residues: 268 loop : -0.22 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 PHE 0.010 0.001 PHE A 866 TYR 0.012 0.002 TYR A 740 ARG 0.009 0.001 ARG B 272 *********************** 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 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.696 Fit side-chains REVERT: A 221 LYS cc_start: 0.7992 (ptpt) cc_final: 0.7644 (ptpp) REVERT: A 224 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: A 262 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7830 (mtmm) REVERT: A 268 ASP cc_start: 0.7253 (p0) cc_final: 0.7025 (p0) REVERT: A 290 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: A 644 ASN cc_start: 0.7568 (m-40) cc_final: 0.7329 (p0) REVERT: A 657 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7002 (OUTLIER) REVERT: A 676 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: A 830 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.5950 (tpp) REVERT: A 848 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6946 (m-70) REVERT: B 118 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6697 (p0) REVERT: B 291 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7179 (mmt-90) REVERT: B 808 ASP cc_start: 0.8355 (m-30) cc_final: 0.7980 (m-30) REVERT: B 836 VAL cc_start: 0.2961 (OUTLIER) cc_final: 0.2724 (t) outliers start: 33 outliers final: 18 residues processed: 212 average time/residue: 1.4656 time to fit residues: 340.0010 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 : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14958 Z= 0.201 Angle : 0.524 8.947 20463 Z= 0.268 Chirality : 0.041 0.177 2298 Planarity : 0.004 0.048 2418 Dihedral : 14.306 85.255 2702 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.23 % Allowed : 15.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1638 helix: 1.51 (0.20), residues: 648 sheet: 0.21 (0.31), residues: 268 loop : -0.14 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 PHE 0.010 0.001 PHE A 800 TYR 0.019 0.001 TYR B 309 ARG 0.010 0.000 ARG B 272 *********************** 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 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.809 Fit side-chains REVERT: A 221 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7601 (ptpp) REVERT: A 224 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7384 (mm-40) REVERT: A 262 LYS cc_start: 0.8278 (ptpp) cc_final: 0.7805 (mtmm) REVERT: A 290 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: A 657 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7019 (OUTLIER) REVERT: A 676 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 830 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.5767 (tpp) REVERT: A 848 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6989 (m-70) REVERT: B 272 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7667 (mtm-85) REVERT: B 778 ARG cc_start: 0.6367 (mmt90) cc_final: 0.6131 (mmt-90) REVERT: B 836 VAL cc_start: 0.2981 (OUTLIER) cc_final: 0.2744 (t) outliers start: 33 outliers final: 13 residues processed: 210 average time/residue: 1.5322 time to fit residues: 349.8062 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS 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 713 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 479 GLN B 38 GLN B 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14958 Z= 0.311 Angle : 0.574 8.525 20463 Z= 0.293 Chirality : 0.043 0.195 2298 Planarity : 0.005 0.061 2418 Dihedral : 14.335 85.081 2702 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.77 % Allowed : 14.82 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1638 helix: 1.34 (0.20), residues: 648 sheet: 0.26 (0.31), residues: 264 loop : -0.22 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.005 0.001 HIS A 389 PHE 0.013 0.001 PHE A 800 TYR 0.013 0.002 TYR B 582 ARG 0.007 0.001 ARG B 272 *********************** 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 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.628 Fit side-chains REVERT: A 221 LYS cc_start: 0.8018 (ptpt) cc_final: 0.7686 (ptpp) REVERT: A 224 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7430 (mm-40) REVERT: A 262 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7801 (mtmm) REVERT: A 290 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: A 657 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7120 (mp0) REVERT: A 676 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: A 830 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5690 (tpp) REVERT: A 848 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7012 (m-70) REVERT: B 118 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.6728 (p0) REVERT: B 146 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (mtm180) REVERT: B 778 ARG cc_start: 0.6333 (mmt90) cc_final: 0.6102 (mmt-90) outliers start: 41 outliers final: 19 residues processed: 209 average time/residue: 1.4442 time to fit residues: 329.5346 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 99 GLN ** B 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14958 Z= 0.181 Angle : 0.522 9.361 20463 Z= 0.270 Chirality : 0.040 0.176 2298 Planarity : 0.004 0.043 2418 Dihedral : 14.283 83.403 2702 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.89 % Allowed : 15.76 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1638 helix: 1.51 (0.20), residues: 648 sheet: 0.30 (0.32), residues: 254 loop : -0.11 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 PHE 0.019 0.001 PHE A 800 TYR 0.019 0.001 TYR B 309 ARG 0.012 0.000 ARG B 272 *********************** 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: 28 poor density : 186 time to evaluate : 1.629 Fit side-chains REVERT: A 224 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7371 (mm-40) REVERT: A 262 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7805 (mtmm) REVERT: A 290 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: A 676 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: A 830 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5572 (tpp) REVERT: A 848 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6934 (m-70) REVERT: A 894 TYR cc_start: 0.8206 (m-80) cc_final: 0.7987 (m-80) REVERT: B 272 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7625 (mtm-85) REVERT: B 690 ARG cc_start: 0.7448 (mpt-90) cc_final: 0.7232 (mpt-90) outliers start: 28 outliers final: 13 residues processed: 203 average time/residue: 1.5284 time to fit residues: 339.1276 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 chunk 161 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 38 GLN B 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14958 Z= 0.183 Angle : 0.538 9.505 20463 Z= 0.276 Chirality : 0.040 0.152 2298 Planarity : 0.004 0.045 2418 Dihedral : 14.236 80.083 2702 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.76 % Allowed : 16.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1638 helix: 1.60 (0.20), residues: 648 sheet: 0.35 (0.32), residues: 254 loop : -0.03 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS B 848 PHE 0.023 0.001 PHE A 800 TYR 0.012 0.001 TYR A 740 ARG 0.009 0.000 ARG B 272 *********************** 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 218 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.681 Fit side-chains REVERT: A 224 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7376 (mm-40) REVERT: A 262 LYS cc_start: 0.8253 (ptpp) cc_final: 0.7847 (mtmm) REVERT: A 290 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: A 676 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 830 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.5492 (tpp) REVERT: A 848 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6923 (m-70) REVERT: A 885 LEU cc_start: 0.8427 (tp) cc_final: 0.8226 (tm) REVERT: B 146 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7854 (mtm180) REVERT: B 272 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7617 (mtm-85) REVERT: B 778 ARG cc_start: 0.6596 (mmt90) cc_final: 0.6184 (mmt-90) outliers start: 26 outliers final: 11 residues processed: 208 average time/residue: 1.4628 time to fit residues: 332.0652 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 397 LEU 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 146 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 0.0470 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 38 GLN B 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 14958 Z= 0.158 Angle : 0.523 9.332 20463 Z= 0.270 Chirality : 0.040 0.152 2298 Planarity : 0.004 0.040 2418 Dihedral : 14.187 77.012 2701 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.22 % Allowed : 17.52 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1638 helix: 1.67 (0.20), residues: 650 sheet: 0.36 (0.32), residues: 274 loop : 0.05 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.003 0.001 HIS A 625 PHE 0.028 0.001 PHE A 800 TYR 0.022 0.001 TYR B 309 ARG 0.010 0.000 ARG B 272 ********************** 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 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.609 Fit side-chains REVERT: A 191 ASP cc_start: 0.7982 (t0) cc_final: 0.7712 (t0) REVERT: A 221 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7476 (ptpp) REVERT: A 262 LYS cc_start: 0.8223 (ptpp) cc_final: 0.7834 (mtmm) REVERT: A 290 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: A 656 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7254 (ptp90) REVERT: A 676 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 830 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5351 (tpp) REVERT: A 848 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: B 146 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7832 (mtm180) REVERT: B 203 GLU cc_start: 0.7729 (tt0) cc_final: 0.7528 (tt0) REVERT: B 272 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7639 (mtm-85) REVERT: B 311 TYR cc_start: 0.7802 (m-80) cc_final: 0.7379 (m-80) REVERT: B 761 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7582 (tp) REVERT: B 778 ARG cc_start: 0.6560 (mmt90) cc_final: 0.6168 (mmt-90) outliers start: 18 outliers final: 9 residues processed: 202 average time/residue: 1.5037 time to fit residues: 330.6228 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 290 GLN Chi-restraints excluded: chain A residue 397 LEU 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 146 ARG Chi-restraints excluded: chain B residue 192 LEU 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 761 LEU Chi-restraints excluded: chain B residue 819 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 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123959 restraints weight = 16575.080| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.82 r_work: 0.3145 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14958 Z= 0.196 Angle : 0.533 9.507 20463 Z= 0.274 Chirality : 0.040 0.152 2298 Planarity : 0.004 0.044 2418 Dihedral : 14.177 74.986 2701 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.49 % Allowed : 17.52 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1638 helix: 1.60 (0.20), residues: 650 sheet: 0.21 (0.32), residues: 264 loop : 0.03 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS B 848 PHE 0.011 0.001 PHE B 585 TYR 0.019 0.001 TYR B 309 ARG 0.009 0.000 ARG B 778 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5682.57 seconds wall clock time: 103 minutes 5.81 seconds (6185.81 seconds total)