Starting phenix.real_space_refine on Thu Jun 12 23:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmx_51457/06_2025/9gmx_51457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmx_51457/06_2025/9gmx_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_51457/06_2025/9gmx_51457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmx_51457/06_2025/9gmx_51457.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmx_51457/06_2025/9gmx_51457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmx_51457/06_2025/9gmx_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.26, per 1000 atoms: 0.64 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 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: 5.14 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: 5.70 Time building geometry restraints manager: 4.09 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: 8.770 Set stop_for_unknowns flag: 0.010 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.850 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.180 ------------------------------------------------------------------------------- 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 14966 Z= 0.352 Angle : 0.707 10.297 20469 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 Details of bonding type rmsd hydrogen bonds : bond 0.12562 ( 646) hydrogen bonds : angle 5.57273 ( 1789) metal coordination : bond 0.00640 ( 8) metal coordination : angle 1.67084 ( 6) covalent geometry : bond 0.00725 (14958) covalent geometry : angle 0.70656 (20463) *********************** 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 : 1.609 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: 1.5461 time to fit residues: 332.9956 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 : 1.617 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124801 restraints weight = 16625.664| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.88 r_work: 0.3185 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 14966 Z= 0.130 Angle : 0.539 8.237 20469 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 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 646) hydrogen bonds : angle 4.59456 ( 1789) metal coordination : bond 0.00729 ( 8) metal coordination : angle 1.82535 ( 6) covalent geometry : bond 0.00285 (14958) covalent geometry : angle 0.53841 (20463) *********************** 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 : 1.662 Fit side-chains REVERT: A 221 LYS cc_start: 0.7775 (tptp) cc_final: 0.7513 (tptp) REVERT: A 268 ASP cc_start: 0.7418 (p0) cc_final: 0.7020 (p0) REVERT: A 657 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6781 (OUTLIER) REVERT: A 661 HIS cc_start: 0.6400 (p-80) cc_final: 0.6141 (p90) REVERT: A 848 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7623 (m-70) REVERT: B 198 TYR cc_start: 0.6762 (p90) cc_final: 0.6543 (p90) REVERT: B 304 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7424 (ptpt) REVERT: B 720 ASP cc_start: 0.7367 (t0) cc_final: 0.7026 (m-30) REVERT: B 836 VAL cc_start: 0.3322 (OUTLIER) cc_final: 0.3104 (t) outliers start: 25 outliers final: 10 residues processed: 216 average time/residue: 1.4877 time to fit residues: 354.5253 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 : 1.678 ------------------------------------------------------------------------------- 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 87 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3836 r_free = 0.3836 target = 0.159841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119844 restraints weight = 16702.764| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.87 r_work: 0.3100 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14966 Z= 0.190 Angle : 0.564 8.522 20469 Z= 0.292 Chirality : 0.043 0.143 2298 Planarity : 0.005 0.065 2418 Dihedral : 14.435 89.598 2702 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.23 % Allowed : 12.45 % Favored : 85.32 % 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: 0.63 (0.20), residues: 1638 helix: 1.31 (0.20), residues: 642 sheet: 0.29 (0.31), residues: 268 loop : -0.25 (0.22), residues: 728 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 0.012 0.002 TYR B 582 ARG 0.010 0.001 ARG B 626 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 646) hydrogen bonds : angle 4.51400 ( 1789) metal coordination : bond 0.00498 ( 8) metal coordination : angle 0.93728 ( 6) covalent geometry : bond 0.00448 (14958) covalent geometry : angle 0.56375 (20463) *********************** 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 : 2.059 Fit side-chains REVERT: A 224 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: A 268 ASP cc_start: 0.7405 (p0) cc_final: 0.7029 (p0) REVERT: A 657 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6892 (OUTLIER) REVERT: A 661 HIS cc_start: 0.6380 (p-80) cc_final: 0.6144 (p90) REVERT: A 676 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 848 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7583 (m-70) REVERT: B 198 TYR cc_start: 0.6762 (p90) cc_final: 0.6547 (p90) REVERT: B 808 ASP cc_start: 0.8578 (m-30) cc_final: 0.8240 (m-30) REVERT: B 836 VAL cc_start: 0.3246 (OUTLIER) cc_final: 0.3034 (t) outliers start: 33 outliers final: 12 residues processed: 211 average time/residue: 1.4216 time to fit residues: 326.9244 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121263 restraints weight = 16677.407| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.85 r_work: 0.3121 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1510 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= 0.152 Angle : 0.529 8.463 20469 Z= 0.274 Chirality : 0.041 0.137 2298 Planarity : 0.004 0.053 2418 Dihedral : 14.377 88.458 2702 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.58 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: 0.67 (0.20), residues: 1638 helix: 1.35 (0.20), residues: 648 sheet: 0.23 (0.31), residues: 268 loop : -0.21 (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 291 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 646) hydrogen bonds : angle 4.40840 ( 1789) metal coordination : bond 0.00178 ( 8) metal coordination : angle 0.97574 ( 6) covalent geometry : bond 0.00355 (14958) covalent geometry : angle 0.52918 (20463) *********************** 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 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.477 Fit side-chains REVERT: A 224 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7591 (mm-40) REVERT: A 262 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7835 (mtmm) REVERT: A 657 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6958 (OUTLIER) REVERT: A 676 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 830 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5716 (tpp) REVERT: A 848 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (m-70) REVERT: B 808 ASP cc_start: 0.8554 (m-30) cc_final: 0.8232 (m-30) outliers start: 30 outliers final: 13 residues processed: 213 average time/residue: 1.5186 time to fit residues: 352.2480 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 : 2.657 ------------------------------------------------------------------------------- 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 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 101 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122497 restraints weight = 16785.491| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.89 r_work: 0.3127 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14966 Z= 0.145 Angle : 0.525 8.324 20469 Z= 0.271 Chirality : 0.041 0.138 2298 Planarity : 0.004 0.051 2418 Dihedral : 14.333 86.427 2702 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.69 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 (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: 0.73 (0.20), residues: 1638 helix: 1.42 (0.20), residues: 648 sheet: 0.22 (0.31), residues: 268 loop : -0.17 (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 B 800 TYR 0.016 0.001 TYR B 198 ARG 0.009 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 646) hydrogen bonds : angle 4.37047 ( 1789) metal coordination : bond 0.00179 ( 8) metal coordination : angle 0.82385 ( 6) covalent geometry : bond 0.00340 (14958) covalent geometry : angle 0.52479 (20463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 2.596 Fit side-chains REVERT: A 224 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7576 (mm-40) REVERT: A 262 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7865 (mtmm) REVERT: A 268 ASP cc_start: 0.7364 (p0) cc_final: 0.7121 (p0) REVERT: A 290 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: A 621 HIS cc_start: 0.7530 (m90) cc_final: 0.7152 (m90) REVERT: A 657 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7008 (OUTLIER) REVERT: A 676 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 830 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.5900 (tpp) REVERT: A 848 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7515 (m-70) REVERT: B 118 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.6785 (p0) REVERT: B 690 ARG cc_start: 0.7478 (mpt-90) cc_final: 0.7204 (mpt-90) REVERT: B 836 VAL cc_start: 0.3077 (OUTLIER) cc_final: 0.2843 (t) outliers start: 33 outliers final: 13 residues processed: 206 average time/residue: 1.7087 time to fit residues: 387.3470 Evaluate side-chains 196 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 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 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 91 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 0.0370 chunk 82 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 ** 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 = 0.3872 r_free = 0.3872 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123672 restraints weight = 16859.341| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.88 r_work: 0.3152 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14966 Z= 0.115 Angle : 0.507 9.306 20469 Z= 0.259 Chirality : 0.040 0.150 2298 Planarity : 0.004 0.040 2418 Dihedral : 14.268 83.543 2702 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.76 % Allowed : 15.43 % 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: 0.95 (0.21), residues: 1638 helix: 1.63 (0.20), residues: 648 sheet: 0.30 (0.31), residues: 268 loop : -0.07 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.004 0.001 HIS B 848 PHE 0.012 0.001 PHE A 800 TYR 0.018 0.001 TYR B 309 ARG 0.009 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 646) hydrogen bonds : angle 4.26269 ( 1789) metal coordination : bond 0.00345 ( 8) metal coordination : angle 1.00209 ( 6) covalent geometry : bond 0.00265 (14958) covalent geometry : angle 0.50656 (20463) *********************** 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 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 1.469 Fit side-chains REVERT: A 224 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: A 262 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7843 (mtmm) REVERT: A 290 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: A 429 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8138 (ttpt) REVERT: A 644 ASN cc_start: 0.7648 (m-40) cc_final: 0.7348 (p0) REVERT: A 657 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7052 (OUTLIER) REVERT: A 676 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: A 830 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.5658 (tpp) REVERT: A 848 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: B 272 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7635 (mtm-85) REVERT: B 894 TYR cc_start: 0.6620 (m-80) cc_final: 0.6161 (m-80) outliers start: 26 outliers final: 11 residues processed: 212 average time/residue: 1.4134 time to fit residues: 326.7825 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 197 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3840 r_free = 0.3840 target = 0.160047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120639 restraints weight = 16834.806| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.92 r_work: 0.3098 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14966 Z= 0.206 Angle : 0.570 8.468 20469 Z= 0.290 Chirality : 0.043 0.195 2298 Planarity : 0.004 0.061 2418 Dihedral : 14.310 83.607 2702 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.71 % Allowed : 15.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.20), residues: 1638 helix: 1.38 (0.20), residues: 648 sheet: 0.35 (0.31), residues: 264 loop : -0.15 (0.23), 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 0.012 0.001 PHE A 800 TYR 0.014 0.002 TYR B 582 ARG 0.006 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 646) hydrogen bonds : angle 4.42747 ( 1789) metal coordination : bond 0.01000 ( 8) metal coordination : angle 0.75694 ( 6) covalent geometry : bond 0.00489 (14958) covalent geometry : angle 0.57009 (20463) *********************** 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 226 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.457 Fit side-chains REVERT: A 224 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7640 (mm-40) REVERT: A 262 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7824 (mtmm) REVERT: A 290 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: A 644 ASN cc_start: 0.7637 (m-40) cc_final: 0.7346 (p0) REVERT: A 657 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7091 (mp0) REVERT: A 676 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: A 830 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5536 (tpp) REVERT: A 848 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7572 (m-70) REVERT: B 118 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.6761 (p0) REVERT: B 778 ARG cc_start: 0.6435 (mmt90) cc_final: 0.6124 (mmt-90) outliers start: 40 outliers final: 16 residues processed: 213 average time/residue: 1.4125 time to fit residues: 328.9057 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123627 restraints weight = 16609.298| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.86 r_work: 0.3146 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14966 Z= 0.120 Angle : 0.520 9.478 20469 Z= 0.268 Chirality : 0.040 0.179 2298 Planarity : 0.004 0.043 2418 Dihedral : 14.264 82.138 2702 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 16.31 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.21), residues: 1638 helix: 1.54 (0.20), residues: 648 sheet: 0.38 (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 332 HIS 0.005 0.001 HIS B 848 PHE 0.020 0.001 PHE A 800 TYR 0.011 0.001 TYR A 740 ARG 0.012 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 646) hydrogen bonds : angle 4.31536 ( 1789) metal coordination : bond 0.00156 ( 8) metal coordination : angle 0.75059 ( 6) covalent geometry : bond 0.00276 (14958) covalent geometry : angle 0.52022 (20463) *********************** 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 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.630 Fit side-chains REVERT: A 224 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7590 (mm-40) REVERT: A 262 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7838 (mtmm) REVERT: A 290 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: A 644 ASN cc_start: 0.7577 (m-40) cc_final: 0.7351 (p0) REVERT: A 657 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7115 (OUTLIER) REVERT: A 676 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 830 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5454 (tpp) REVERT: A 848 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7506 (m-70) REVERT: B 146 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7962 (mtm180) REVERT: B 272 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7665 (mtm-85) REVERT: B 778 ARG cc_start: 0.6388 (mmt90) cc_final: 0.6077 (mmt-90) REVERT: B 894 TYR cc_start: 0.6497 (m-80) cc_final: 0.6014 (m-80) outliers start: 28 outliers final: 11 residues processed: 200 average time/residue: 1.6909 time to fit residues: 368.1395 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain B residue 146 ARG 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 125 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122550 restraints weight = 16683.757| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.91 r_work: 0.3120 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14966 Z= 0.156 Angle : 0.546 9.227 20469 Z= 0.280 Chirality : 0.041 0.202 2298 Planarity : 0.004 0.051 2418 Dihedral : 14.256 80.628 2702 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.62 % Allowed : 16.71 % Favored : 81.66 % 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: 0.87 (0.21), residues: 1638 helix: 1.47 (0.20), residues: 650 sheet: 0.23 (0.32), residues: 264 loop : -0.01 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS B 848 PHE 0.027 0.001 PHE A 800 TYR 0.016 0.001 TYR B 309 ARG 0.010 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 646) hydrogen bonds : angle 4.36319 ( 1789) metal coordination : bond 0.00447 ( 8) metal coordination : angle 0.64198 ( 6) covalent geometry : bond 0.00367 (14958) covalent geometry : angle 0.54592 (20463) *********************** 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 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 2.163 Fit side-chains REVERT: A 224 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: A 262 LYS cc_start: 0.8311 (ptpp) cc_final: 0.7837 (mtmm) REVERT: A 290 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: A 644 ASN cc_start: 0.7564 (m-40) cc_final: 0.7343 (p0) REVERT: A 657 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7127 (mp0) REVERT: A 676 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: A 830 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5436 (tpp) REVERT: A 848 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: B 146 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (mtm180) REVERT: B 272 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7670 (mtm-85) REVERT: B 778 ARG cc_start: 0.6344 (mmt90) cc_final: 0.6076 (mmt-90) outliers start: 24 outliers final: 11 residues processed: 203 average time/residue: 1.9365 time to fit residues: 428.8891 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 : 1.808 ------------------------------------------------------------------------------- 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 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 146 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122627 restraints weight = 16708.994| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.94 r_work: 0.3121 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14966 Z= 0.160 Angle : 0.561 9.252 20469 Z= 0.287 Chirality : 0.041 0.155 2298 Planarity : 0.004 0.050 2418 Dihedral : 14.255 80.099 2702 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 (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: 0.83 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 650 sheet: 0.20 (0.32), residues: 264 loop : -0.00 (0.23), residues: 724 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 0.011 0.001 PHE A 223 TYR 0.013 0.001 TYR B 629 ARG 0.009 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 646) hydrogen bonds : angle 4.38234 ( 1789) metal coordination : bond 0.00469 ( 8) metal coordination : angle 0.61953 ( 6) covalent geometry : bond 0.00377 (14958) covalent geometry : angle 0.56085 (20463) ********************** 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 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.525 Fit side-chains REVERT: A 224 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: A 262 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7826 (mtmm) REVERT: A 290 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: A 644 ASN cc_start: 0.7561 (m-40) cc_final: 0.7346 (p0) REVERT: A 657 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7184 (mp0) REVERT: A 676 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: A 830 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5296 (tpp) REVERT: A 848 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7490 (m-70) REVERT: B 146 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7968 (mtm180) REVERT: B 272 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7722 (mtm-85) REVERT: B 720 ASP cc_start: 0.7690 (m-30) cc_final: 0.7488 (t0) REVERT: B 778 ARG cc_start: 0.6321 (mmt90) cc_final: 0.6064 (mmt-90) outliers start: 25 outliers final: 13 residues processed: 199 average time/residue: 1.4782 time to fit residues: 320.5926 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 848 HIS Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain B residue 146 ARG 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 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 46 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 100 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.163741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125039 restraints weight = 16743.845| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.93 r_work: 0.3162 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14966 Z= 0.112 Angle : 0.528 11.406 20469 Z= 0.270 Chirality : 0.040 0.152 2298 Planarity : 0.004 0.038 2418 Dihedral : 14.198 77.498 2702 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.49 % Allowed : 17.05 % Favored : 81.46 % 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: 1.02 (0.21), residues: 1638 helix: 1.56 (0.20), residues: 652 sheet: 0.33 (0.32), residues: 284 loop : 0.10 (0.24), residues: 702 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 0.018 0.001 PHE A 800 TYR 0.019 0.001 TYR B 309 ARG 0.010 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 646) hydrogen bonds : angle 4.28355 ( 1789) metal coordination : bond 0.00310 ( 8) metal coordination : angle 0.81831 ( 6) covalent geometry : bond 0.00258 (14958) covalent geometry : angle 0.52832 (20463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12895.61 seconds wall clock time: 228 minutes 0.67 seconds (13680.67 seconds total)