Starting phenix.real_space_refine on Mon Jan 20 00:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ere_19913/01_2025/9ere_19913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ere_19913/01_2025/9ere_19913.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/9ere_19913/01_2025/9ere_19913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ere_19913/01_2025/9ere_19913.map" model { file = "/net/cci-nas-00/data/ceres_data/9ere_19913/01_2025/9ere_19913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ere_19913/01_2025/9ere_19913.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= -0.001 sd= 0.125 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 3 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 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14541 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 73.993 60.501 71.377 1.00 55.34 S ATOM 2393 SG CYS A 321 73.713 59.016 67.866 1.00 50.25 S ATOM 2399 SG CYS A 322 71.160 61.546 69.077 1.00 53.20 S ATOM 8781 SG CYS B 287 22.980 71.162 71.471 1.00 62.19 S ATOM 9058 SG CYS B 321 22.983 72.191 67.850 1.00 47.88 S ATOM 9064 SG CYS B 322 25.569 69.827 69.210 1.00 48.25 S Time building chain proxies: 9.54, per 1000 atoms: 0.66 Number of scatterers: 14541 At special positions: 0 Unit cell: (97.557, 132.174, 145.811, 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 3 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: 3.75 Conformation dependent library (CDL) restraints added in 1.7 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 18 sheets defined 44.6% alpha, 19.2% beta 23 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 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 93 removed outlier: 4.186A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.540A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 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: 5.547A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.133A 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: 4.513A 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: 3.589A 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 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 757 through 763 removed outlier: 4.309A pdb=" N LEU A 761 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) 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 818 through 831 removed outlier: 3.648A 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 855 through 858 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.579A 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 89 through 93 removed outlier: 4.284A pdb=" N PHE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 222 through 241 removed outlier: 4.085A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix 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: 3.655A 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: 5.668A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.155A 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 480 through 501 removed outlier: 4.484A pdb=" N GLN B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 4.538A 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 removed outlier: 3.626A pdb=" N ARG B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) 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 removed outlier: 3.638A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.507A pdb=" N GLN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 763 removed outlier: 3.771A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 762 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (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 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 Processing helix chain 'B' and resid 878 through 887 removed outlier: 4.309A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.663A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.299A 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: 5.425A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.425A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.237A 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 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: 6.512A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.166A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 595 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 702 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 597 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.105A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 810 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE A 868 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 812 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 11 removed outlier: 4.616A pdb=" N VAL B 18 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL B 21 " --> 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: 6.796A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.204A 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: 6.796A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.497A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.486A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.062A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 810 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 868 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 812 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 598 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 21 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2226 1.28 - 1.41: 3908 1.41 - 1.55: 8591 1.55 - 1.68: 111 1.68 - 1.81: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ARG B 729 " pdb=" C ARG B 729 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.24e-02 6.50e+03 7.03e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.234 1.148 0.087 1.26e-02 6.30e+03 4.72e+01 bond pdb=" C ARG A 862 " pdb=" O ARG A 862 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.22e-02 6.72e+03 3.04e+01 bond pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.82e+01 bond pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.21e-02 6.83e+03 2.35e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19984 1.78 - 3.56: 398 3.56 - 5.35: 68 5.35 - 7.13: 10 7.13 - 8.91: 3 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.71 120.44 -8.73 1.15e+00 7.56e-01 5.77e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 111.28 117.35 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" C GLN A 774 " ideal model delta sigma weight residual 110.20 118.26 -8.06 1.58e+00 4.01e-01 2.60e+01 angle pdb=" C PRO A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.84 113.57 6.27 1.25e+00 6.40e-01 2.51e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8229 19.09 - 38.18: 626 38.18 - 57.26: 221 57.26 - 76.35: 105 76.35 - 95.44: 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 232.00 136.56 95.44 1 1.70e+01 3.46e-03 3.64e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C ARG B 729 " pdb=" N ARG B 729 " pdb=" CA ARG B 729 " pdb=" CB ARG B 729 " ideal model delta harmonic sigma weight residual -122.60 -112.06 -10.54 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2067 0.067 - 0.134: 221 0.134 - 0.202: 6 0.202 - 0.269: 3 0.269 - 0.336: 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 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN A 706 " pdb=" N GLN A 706 " pdb=" C GLN A 706 " pdb=" CB GLN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 705 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 705 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE A 705 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 706 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 851 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LEU A 851 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 851 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 852 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C THR B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O THR B 728 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 729 " -0.018 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 10482 3.10 - 3.70: 23246 3.70 - 4.30: 35303 4.30 - 4.90: 57539 Nonbonded interactions: 126660 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 1.903 2.320 nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.918 2.170 nonbonded pdb=" OD2 ASP A 252 " pdb="MN MN A1002 " model vdw 1.927 2.320 nonbonded pdb=" OE2 GLU A 209 " pdb="MN MN A1002 " model vdw 2.051 2.320 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 2.062 2.320 ... (remaining 126655 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' and (resid 7 through 899 or resid 1001 through 1002)) } 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 42.150 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.005 0.104 14958 Z= 0.314 Angle : 0.641 8.911 20463 Z= 0.368 Chirality : 0.042 0.336 2298 Planarity : 0.006 0.084 2418 Dihedral : 17.120 95.438 6075 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.61 % Allowed : 11.91 % Favored : 87.48 % 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: 0.59 (0.20), residues: 1638 helix: 0.97 (0.20), residues: 662 sheet: -0.22 (0.30), residues: 256 loop : 0.26 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 332 HIS 0.009 0.001 HIS A 661 PHE 0.021 0.001 PHE A 620 TYR 0.020 0.001 TYR B 681 ARG 0.012 0.001 ARG A 414 *********************** 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 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8879 (mmm) cc_final: 0.8329 (mmm) REVERT: A 414 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6748 (mtm110) REVERT: A 689 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6286 (mtm-85) REVERT: A 786 GLU cc_start: 0.7176 (mp0) cc_final: 0.6968 (pm20) REVERT: A 848 HIS cc_start: 0.7761 (m-70) cc_final: 0.7351 (m90) REVERT: B 145 SER cc_start: 0.8773 (m) cc_final: 0.8562 (m) REVERT: B 594 GLU cc_start: 0.7553 (mp0) cc_final: 0.7226 (mp0) REVERT: B 729 ARG cc_start: 0.8456 (mpp-170) cc_final: 0.8159 (mmt-90) REVERT: B 794 ASP cc_start: 0.7020 (t70) cc_final: 0.6632 (t0) outliers start: 9 outliers final: 4 residues processed: 216 average time/residue: 1.6898 time to fit residues: 394.3370 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 637 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 625 HIS A 638 ASN B 195 GLN B 663 GLN B 848 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120929 restraints weight = 15166.536| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.86 r_work: 0.3092 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14958 Z= 0.292 Angle : 0.577 8.543 20463 Z= 0.299 Chirality : 0.042 0.155 2298 Planarity : 0.005 0.062 2418 Dihedral : 14.750 97.174 2710 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.98 % Allowed : 11.64 % Favored : 85.39 % 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 (0.21), residues: 1638 helix: 1.16 (0.20), residues: 654 sheet: -0.61 (0.30), residues: 244 loop : 0.35 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 PHE 0.014 0.002 PHE A 435 TYR 0.021 0.002 TYR B 681 ARG 0.007 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 246 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 200 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: A 219 SER cc_start: 0.8922 (t) cc_final: 0.8664 (p) REVERT: A 290 GLN cc_start: 0.8222 (mt0) cc_final: 0.8004 (mp10) REVERT: A 291 ARG cc_start: 0.7578 (pmm-80) cc_final: 0.7376 (pmm-80) REVERT: A 385 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (mmtm) REVERT: A 453 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: A 482 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6243 (tm-30) REVERT: A 485 ASP cc_start: 0.8593 (t70) cc_final: 0.8253 (t0) REVERT: A 729 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7974 (mtt90) REVERT: A 818 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6630 (mp0) REVERT: A 848 HIS cc_start: 0.8152 (m-70) cc_final: 0.7651 (m90) REVERT: B 11 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: B 38 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: B 198 TYR cc_start: 0.7807 (p90) cc_final: 0.7523 (p90) REVERT: B 262 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7579 (ptpt) REVERT: B 428 ASN cc_start: 0.8696 (m-40) cc_final: 0.8303 (m-40) REVERT: B 479 GLN cc_start: 0.8342 (tp40) cc_final: 0.7562 (mp10) REVERT: B 594 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 608 MET cc_start: 0.8740 (mmt) cc_final: 0.8526 (mmt) REVERT: B 617 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7650 (ptm160) REVERT: B 677 ASP cc_start: 0.7696 (t0) cc_final: 0.7471 (t0) REVERT: B 745 MET cc_start: 0.7748 (mtp) cc_final: 0.7537 (mtp) REVERT: B 794 ASP cc_start: 0.7262 (t70) cc_final: 0.6825 (t0) outliers start: 44 outliers final: 12 residues processed: 229 average time/residue: 1.5411 time to fit residues: 383.3979 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 224 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119090 restraints weight = 15238.861| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.89 r_work: 0.3050 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14958 Z= 0.306 Angle : 0.561 8.560 20463 Z= 0.289 Chirality : 0.042 0.155 2298 Planarity : 0.005 0.055 2418 Dihedral : 14.597 93.759 2705 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.98 % Allowed : 12.72 % Favored : 84.30 % 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: 0.59 (0.21), residues: 1638 helix: 1.08 (0.20), residues: 658 sheet: -0.68 (0.31), residues: 244 loop : 0.33 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.007 0.001 HIS A 661 PHE 0.011 0.002 PHE B 151 TYR 0.020 0.002 TYR B 681 ARG 0.013 0.001 ARG A 414 *********************** 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 240 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: A 200 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: A 219 SER cc_start: 0.8936 (t) cc_final: 0.8726 (p) REVERT: A 290 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: A 335 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: A 351 MET cc_start: 0.9019 (mmm) cc_final: 0.8667 (mmm) REVERT: A 453 GLU cc_start: 0.8077 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 482 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6426 (tm-30) REVERT: A 485 ASP cc_start: 0.8685 (t70) cc_final: 0.8364 (t0) REVERT: A 649 GLU cc_start: 0.7973 (mp0) cc_final: 0.7575 (mp0) REVERT: A 729 ARG cc_start: 0.8264 (mtt90) cc_final: 0.8037 (mtt90) REVERT: A 830 MET cc_start: 0.7531 (tpp) cc_final: 0.6873 (mmm) REVERT: A 848 HIS cc_start: 0.8160 (m-70) cc_final: 0.7686 (m90) REVERT: B 11 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 38 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: B 195 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8173 (mm110) REVERT: B 198 TYR cc_start: 0.7855 (p90) cc_final: 0.7591 (p90) REVERT: B 233 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: B 428 ASN cc_start: 0.8794 (m-40) cc_final: 0.8349 (m-40) REVERT: B 479 GLN cc_start: 0.8371 (tp40) cc_final: 0.7502 (mp10) REVERT: B 594 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 608 MET cc_start: 0.8741 (mmt) cc_final: 0.8530 (mmt) REVERT: B 617 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7550 (ptm160) REVERT: B 677 ASP cc_start: 0.7839 (t0) cc_final: 0.7598 (t0) REVERT: B 745 MET cc_start: 0.7652 (mtp) cc_final: 0.7431 (mtp) REVERT: B 794 ASP cc_start: 0.7291 (t70) cc_final: 0.6844 (t0) REVERT: B 808 ASP cc_start: 0.8652 (m-30) cc_final: 0.8349 (m-30) REVERT: B 837 GLN cc_start: 0.7671 (tp40) cc_final: 0.7120 (tt0) outliers start: 44 outliers final: 18 residues processed: 221 average time/residue: 1.5860 time to fit residues: 379.9091 Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 145 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 195 GLN B 224 GLN B 276 GLN B 420 HIS B 545 GLN B 848 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120820 restraints weight = 15174.533| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.85 r_work: 0.3090 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14958 Z= 0.218 Angle : 0.521 8.475 20463 Z= 0.269 Chirality : 0.040 0.152 2298 Planarity : 0.004 0.053 2418 Dihedral : 14.488 90.625 2705 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.98 % Allowed : 13.53 % Favored : 83.49 % 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: 0.71 (0.21), residues: 1638 helix: 1.24 (0.20), residues: 660 sheet: -0.68 (0.31), residues: 244 loop : 0.35 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 PHE 0.011 0.001 PHE A 620 TYR 0.021 0.001 TYR B 681 ARG 0.013 0.001 ARG A 414 *********************** 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 235 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: A 200 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 290 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: A 335 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: A 337 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8717 (ptmm) REVERT: A 351 MET cc_start: 0.9041 (mmm) cc_final: 0.8540 (mmm) REVERT: A 414 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7059 (mtm110) REVERT: A 431 MET cc_start: 0.8836 (mmt) cc_final: 0.8338 (mmp) REVERT: A 482 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6291 (tm-30) REVERT: A 485 ASP cc_start: 0.8652 (t70) cc_final: 0.8333 (t0) REVERT: A 649 GLU cc_start: 0.7911 (mp0) cc_final: 0.7487 (mp0) REVERT: A 729 ARG cc_start: 0.8258 (mtt90) cc_final: 0.8015 (mtt90) REVERT: A 830 MET cc_start: 0.7485 (tpp) cc_final: 0.6748 (mmm) REVERT: A 848 HIS cc_start: 0.8214 (m-70) cc_final: 0.7754 (m90) REVERT: B 11 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 195 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: B 198 TYR cc_start: 0.7829 (p90) cc_final: 0.7545 (p90) REVERT: B 428 ASN cc_start: 0.8768 (m-40) cc_final: 0.8367 (m-40) REVERT: B 479 GLN cc_start: 0.8344 (tp40) cc_final: 0.7490 (mp10) REVERT: B 594 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 617 ARG cc_start: 0.7938 (ptm160) cc_final: 0.7503 (ptm160) REVERT: B 677 ASP cc_start: 0.7811 (t0) cc_final: 0.7569 (t0) REVERT: B 794 ASP cc_start: 0.7330 (t70) cc_final: 0.6892 (t0) REVERT: B 808 ASP cc_start: 0.8600 (m-30) cc_final: 0.8248 (m-30) outliers start: 44 outliers final: 13 residues processed: 216 average time/residue: 1.5118 time to fit residues: 356.2602 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121281 restraints weight = 15270.644| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.90 r_work: 0.3095 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14958 Z= 0.203 Angle : 0.514 8.322 20463 Z= 0.264 Chirality : 0.040 0.149 2298 Planarity : 0.004 0.039 2418 Dihedral : 14.408 88.141 2702 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.57 % Allowed : 14.75 % 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: 0.78 (0.21), residues: 1638 helix: 1.36 (0.20), residues: 658 sheet: -0.65 (0.31), residues: 244 loop : 0.32 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 PHE 0.016 0.001 PHE A 620 TYR 0.015 0.001 TYR A 234 ARG 0.010 0.001 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 200 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: A 290 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: A 335 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: A 431 MET cc_start: 0.8854 (mmt) cc_final: 0.8371 (mmp) REVERT: A 482 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6226 (tm-30) REVERT: A 485 ASP cc_start: 0.8665 (t70) cc_final: 0.8350 (t0) REVERT: A 649 GLU cc_start: 0.7945 (mp0) cc_final: 0.7499 (mp0) REVERT: A 729 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7786 (mtt90) REVERT: A 830 MET cc_start: 0.7446 (tpp) cc_final: 0.6725 (mmm) REVERT: A 848 HIS cc_start: 0.8211 (m-70) cc_final: 0.7585 (m-70) REVERT: B 11 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: B 198 TYR cc_start: 0.7835 (p90) cc_final: 0.7538 (p90) REVERT: B 428 ASN cc_start: 0.8829 (m-40) cc_final: 0.8461 (m-40) REVERT: B 479 GLN cc_start: 0.8302 (tp40) cc_final: 0.7475 (mp10) REVERT: B 617 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7462 (ptm160) REVERT: B 647 ARG cc_start: 0.8387 (ttt180) cc_final: 0.8183 (ttt180) REVERT: B 656 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.6908 (mtm-85) REVERT: B 677 ASP cc_start: 0.7710 (t0) cc_final: 0.7417 (t0) REVERT: B 794 ASP cc_start: 0.7331 (t70) cc_final: 0.6892 (t0) REVERT: B 808 ASP cc_start: 0.8563 (m-30) cc_final: 0.8164 (m-30) outliers start: 38 outliers final: 16 residues processed: 213 average time/residue: 1.5372 time to fit residues: 356.0755 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121328 restraints weight = 15257.240| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.89 r_work: 0.3116 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14958 Z= 0.212 Angle : 0.515 8.197 20463 Z= 0.264 Chirality : 0.040 0.148 2298 Planarity : 0.004 0.061 2418 Dihedral : 14.366 86.442 2702 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.14 % 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: 0.80 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 658 sheet: -0.61 (0.31), residues: 244 loop : 0.29 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.006 0.001 HIS A 661 PHE 0.010 0.001 PHE A 103 TYR 0.020 0.001 TYR B 681 ARG 0.016 0.001 ARG A 414 *********************** 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 236 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: A 200 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: A 212 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8975 (mt) REVERT: A 335 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 414 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6763 (mtm110) REVERT: A 482 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6206 (tm-30) REVERT: A 485 ASP cc_start: 0.8657 (t70) cc_final: 0.8330 (t0) REVERT: A 649 GLU cc_start: 0.7952 (mp0) cc_final: 0.7492 (mp0) REVERT: A 729 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7815 (mtt90) REVERT: A 830 MET cc_start: 0.7451 (tpp) cc_final: 0.7098 (mmm) REVERT: A 848 HIS cc_start: 0.8214 (m-70) cc_final: 0.7740 (m90) REVERT: B 11 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: B 198 TYR cc_start: 0.7824 (p90) cc_final: 0.7534 (p90) REVERT: B 229 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7022 (ptp-110) REVERT: B 428 ASN cc_start: 0.8833 (m-40) cc_final: 0.8461 (m-40) REVERT: B 479 GLN cc_start: 0.8308 (tp40) cc_final: 0.7466 (mp10) REVERT: B 594 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: B 617 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7438 (ptm160) REVERT: B 647 ARG cc_start: 0.8410 (ttt180) cc_final: 0.8189 (ttp-170) REVERT: B 656 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: B 677 ASP cc_start: 0.7605 (t70) cc_final: 0.7341 (t0) REVERT: B 690 ARG cc_start: 0.6679 (mtm110) cc_final: 0.6350 (mtt90) REVERT: B 794 ASP cc_start: 0.7334 (t70) cc_final: 0.6888 (t0) REVERT: B 808 ASP cc_start: 0.8565 (m-30) cc_final: 0.8212 (m-30) outliers start: 44 outliers final: 19 residues processed: 221 average time/residue: 1.5140 time to fit residues: 363.4859 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121848 restraints weight = 15327.740| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.88 r_work: 0.3130 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14958 Z= 0.215 Angle : 0.516 8.070 20463 Z= 0.265 Chirality : 0.040 0.149 2298 Planarity : 0.004 0.053 2418 Dihedral : 14.336 84.813 2702 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.57 % Allowed : 15.43 % Favored : 82.00 % 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: 0.84 (0.21), residues: 1638 helix: 1.45 (0.20), residues: 658 sheet: -0.57 (0.32), residues: 244 loop : 0.30 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.006 0.001 HIS A 661 PHE 0.010 0.001 PHE A 103 TYR 0.024 0.001 TYR B 681 ARG 0.013 0.001 ARG A 414 *********************** 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 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 200 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: A 212 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 335 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 414 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6758 (mtm110) REVERT: A 482 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6221 (tm-30) REVERT: A 485 ASP cc_start: 0.8680 (t70) cc_final: 0.8371 (t0) REVERT: A 649 GLU cc_start: 0.7991 (mp0) cc_final: 0.7660 (mp0) REVERT: A 729 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7832 (mtt90) REVERT: A 830 MET cc_start: 0.7461 (tpp) cc_final: 0.7045 (mmm) REVERT: A 848 HIS cc_start: 0.8232 (m-70) cc_final: 0.7629 (m-70) REVERT: B 11 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: B 198 TYR cc_start: 0.7810 (p90) cc_final: 0.7488 (p90) REVERT: B 273 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8234 (tttp) REVERT: B 350 MET cc_start: 0.9035 (mtp) cc_final: 0.8809 (mtp) REVERT: B 428 ASN cc_start: 0.8847 (m-40) cc_final: 0.8511 (m-40) REVERT: B 479 GLN cc_start: 0.8310 (tp40) cc_final: 0.7448 (mp10) REVERT: B 594 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 617 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7481 (ptm160) REVERT: B 677 ASP cc_start: 0.7575 (t70) cc_final: 0.7343 (t0) REVERT: B 690 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6365 (mtt90) REVERT: B 794 ASP cc_start: 0.7296 (t70) cc_final: 0.6827 (t0) REVERT: B 808 ASP cc_start: 0.8587 (m-30) cc_final: 0.8208 (m-30) outliers start: 38 outliers final: 20 residues processed: 211 average time/residue: 1.5916 time to fit residues: 365.9433 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 276 GLN B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121530 restraints weight = 15005.556| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.88 r_work: 0.3086 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14958 Z= 0.217 Angle : 0.517 7.872 20463 Z= 0.265 Chirality : 0.040 0.148 2298 Planarity : 0.004 0.054 2418 Dihedral : 14.299 83.642 2702 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.44 % Allowed : 15.49 % Favored : 82.07 % 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: 0.88 (0.21), residues: 1638 helix: 1.48 (0.20), residues: 660 sheet: -0.52 (0.32), residues: 244 loop : 0.30 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 PHE 0.010 0.001 PHE B 435 TYR 0.025 0.001 TYR B 681 ARG 0.014 0.001 ARG A 690 *********************** 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 226 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: A 200 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: A 212 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 268 ASP cc_start: 0.8234 (m-30) cc_final: 0.7996 (m-30) REVERT: A 335 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: A 414 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6741 (mtm110) REVERT: A 482 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6170 (tm-30) REVERT: A 485 ASP cc_start: 0.8656 (t70) cc_final: 0.8323 (t0) REVERT: A 649 GLU cc_start: 0.7962 (mp0) cc_final: 0.7611 (mp0) REVERT: A 729 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7828 (mtt90) REVERT: A 830 MET cc_start: 0.7507 (tpp) cc_final: 0.7185 (mmm) REVERT: A 848 HIS cc_start: 0.8218 (m-70) cc_final: 0.7585 (m-70) REVERT: B 11 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: B 198 TYR cc_start: 0.7793 (p90) cc_final: 0.7518 (p90) REVERT: B 229 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7193 (ptp-110) REVERT: B 273 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8241 (tttp) REVERT: B 350 MET cc_start: 0.9065 (mtp) cc_final: 0.8842 (mtp) REVERT: B 428 ASN cc_start: 0.8843 (m-40) cc_final: 0.8499 (m-40) REVERT: B 479 GLN cc_start: 0.8311 (tp40) cc_final: 0.7437 (mp10) REVERT: B 594 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: B 617 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7395 (ptm160) REVERT: B 626 ARG cc_start: 0.7023 (mmp-170) cc_final: 0.6692 (mmp-170) REVERT: B 677 ASP cc_start: 0.7602 (t70) cc_final: 0.7353 (t0) REVERT: B 794 ASP cc_start: 0.7214 (t70) cc_final: 0.6789 (t0) REVERT: B 808 ASP cc_start: 0.8568 (m-30) cc_final: 0.8117 (m-30) outliers start: 36 outliers final: 18 residues processed: 211 average time/residue: 1.5805 time to fit residues: 362.7527 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 154 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS 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 = 0.168246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123539 restraints weight = 15108.254| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.75 r_work: 0.3127 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14958 Z= 0.207 Angle : 0.517 7.664 20463 Z= 0.264 Chirality : 0.040 0.149 2298 Planarity : 0.005 0.058 2418 Dihedral : 14.268 83.087 2702 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.17 % Allowed : 15.83 % Favored : 82.00 % 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: 0.91 (0.21), residues: 1638 helix: 1.53 (0.20), residues: 660 sheet: -0.51 (0.32), residues: 244 loop : 0.29 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.008 0.001 HIS A 661 PHE 0.011 0.001 PHE B 435 TYR 0.026 0.001 TYR B 681 ARG 0.015 0.001 ARG A 689 *********************** 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: 32 poor density : 186 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: A 200 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: A 268 ASP cc_start: 0.8228 (m-30) cc_final: 0.7995 (m-30) REVERT: A 335 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: A 336 ASP cc_start: 0.7362 (m-30) cc_final: 0.6959 (t70) REVERT: A 337 LYS cc_start: 0.8858 (ptmt) cc_final: 0.8645 (ptmm) REVERT: A 452 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 482 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6189 (tm-30) REVERT: A 485 ASP cc_start: 0.8633 (t70) cc_final: 0.8327 (t0) REVERT: A 649 GLU cc_start: 0.7960 (mp0) cc_final: 0.7615 (mp0) REVERT: A 729 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7827 (mtt90) REVERT: A 830 MET cc_start: 0.7519 (tpp) cc_final: 0.7227 (mmm) REVERT: A 848 HIS cc_start: 0.8227 (m-70) cc_final: 0.7617 (m-70) REVERT: B 11 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: B 198 TYR cc_start: 0.7761 (p90) cc_final: 0.7487 (p90) REVERT: B 229 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7169 (ptp-110) REVERT: B 273 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (tttp) REVERT: B 350 MET cc_start: 0.9060 (mtp) cc_final: 0.8830 (mtp) REVERT: B 428 ASN cc_start: 0.8823 (m-40) cc_final: 0.8485 (m110) REVERT: B 479 GLN cc_start: 0.8319 (tp40) cc_final: 0.7444 (mp10) REVERT: B 594 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: B 617 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7400 (ptm160) REVERT: B 626 ARG cc_start: 0.7039 (mmp-170) cc_final: 0.6715 (mmp-170) REVERT: B 677 ASP cc_start: 0.7603 (t70) cc_final: 0.7359 (t0) REVERT: B 689 ARG cc_start: 0.6866 (mtm110) cc_final: 0.6516 (mmp80) REVERT: B 690 ARG cc_start: 0.6498 (mtm110) cc_final: 0.6185 (mtt90) REVERT: B 794 ASP cc_start: 0.7296 (t70) cc_final: 0.6848 (t0) REVERT: B 808 ASP cc_start: 0.8559 (m-30) cc_final: 0.8238 (m-30) outliers start: 32 outliers final: 17 residues processed: 204 average time/residue: 1.5177 time to fit residues: 337.8251 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.168638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122805 restraints weight = 15182.291| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.87 r_work: 0.3101 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14958 Z= 0.189 Angle : 0.515 7.558 20463 Z= 0.263 Chirality : 0.040 0.149 2298 Planarity : 0.005 0.066 2418 Dihedral : 14.252 82.765 2702 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 16.64 % Favored : 81.73 % 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: 0.93 (0.21), residues: 1638 helix: 1.55 (0.20), residues: 660 sheet: -0.48 (0.32), residues: 244 loop : 0.30 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.008 0.001 HIS B 848 PHE 0.011 0.001 PHE B 435 TYR 0.025 0.001 TYR B 681 ARG 0.015 0.001 ARG A 689 ********************** 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: 24 poor density : 186 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 200 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: A 268 ASP cc_start: 0.8297 (m-30) cc_final: 0.8078 (m-30) REVERT: A 335 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: A 336 ASP cc_start: 0.7395 (m-30) cc_final: 0.6994 (t70) REVERT: A 337 LYS cc_start: 0.8863 (ptmt) cc_final: 0.8650 (ptmm) REVERT: A 482 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6223 (tm-30) REVERT: A 485 ASP cc_start: 0.8668 (t70) cc_final: 0.8360 (t0) REVERT: A 649 GLU cc_start: 0.8002 (mp0) cc_final: 0.7652 (mp0) REVERT: A 729 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7867 (mtt90) REVERT: A 830 MET cc_start: 0.7500 (tpp) cc_final: 0.7215 (mmm) REVERT: A 848 HIS cc_start: 0.8269 (m-70) cc_final: 0.7658 (m-70) REVERT: B 11 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: B 198 TYR cc_start: 0.7765 (p90) cc_final: 0.7498 (p90) REVERT: B 273 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8238 (tttp) REVERT: B 335 GLU cc_start: 0.7797 (pt0) cc_final: 0.7474 (pt0) REVERT: B 428 ASN cc_start: 0.8804 (m-40) cc_final: 0.8465 (m110) REVERT: B 479 GLN cc_start: 0.8315 (tp40) cc_final: 0.7424 (mp10) REVERT: B 594 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: B 617 ARG cc_start: 0.7976 (ptm160) cc_final: 0.7385 (ptm160) REVERT: B 626 ARG cc_start: 0.7023 (mmp-170) cc_final: 0.6711 (mmp-170) REVERT: B 677 ASP cc_start: 0.7615 (t70) cc_final: 0.7367 (t0) REVERT: B 690 ARG cc_start: 0.6577 (mtm110) cc_final: 0.6294 (mtt90) REVERT: B 794 ASP cc_start: 0.7274 (t70) cc_final: 0.6849 (t0) REVERT: B 808 ASP cc_start: 0.8580 (m-30) cc_final: 0.8161 (m-30) outliers start: 24 outliers final: 16 residues processed: 201 average time/residue: 1.5783 time to fit residues: 345.7783 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121693 restraints weight = 15214.636| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.88 r_work: 0.3078 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14958 Z= 0.251 Angle : 0.534 7.411 20463 Z= 0.273 Chirality : 0.040 0.151 2298 Planarity : 0.005 0.084 2418 Dihedral : 14.262 82.577 2702 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 16.51 % Favored : 81.73 % 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: 1.49 (0.20), residues: 660 sheet: -0.49 (0.32), residues: 244 loop : 0.26 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.010 0.001 HIS B 848 PHE 0.013 0.001 PHE A 705 TYR 0.025 0.001 TYR B 681 ARG 0.020 0.001 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11742.43 seconds wall clock time: 209 minutes 38.20 seconds (12578.20 seconds total)