Starting phenix.real_space_refine on Thu Aug 6 08:49:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ere_19913/08_2026/9ere_19913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ere_19913/08_2026/9ere_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_19913/08_2026/9ere_19913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ere_19913/08_2026/9ere_19913.map" model { file = "/net/cci-nas-00/data/ceres_data/9ere_19913/08_2026/9ere_19913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ere_19913/08_2026/9ere_19913.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.99, per 1000 atoms: 0.21 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: 1.09 Conformation dependent library (CDL) restraints added in 542.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 18 sheets defined 44.6% alpha, 19.2% beta 23 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.51 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: 2.77 Time building geometry restraints manager: 1.52 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: 19872 1.78 - 3.56: 510 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: 2010 0.067 - 0.134: 278 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 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 14966 Z= 0.277 Angle : 0.667 8.911 20469 Z= 0.430 Chirality : 0.045 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (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 ARG 0.012 0.001 ARG A 414 TYR 0.020 0.001 TYR B 681 PHE 0.021 0.001 PHE A 620 TRP 0.008 0.002 TRP B 332 HIS 0.009 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.28 (14958) covalent geometry : angle 0.66385 / 0.43 (20463) hydrogen bonds : bond 0.12258 / 9.38 ( 645) hydrogen bonds : angle 5.74508 / 4.19 ( 1789) metal coordination : bond 0.01942 / 2.61 ( 8) metal coordination : angle 3.71606 / 8.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.470 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: 0.6401 time to fit residues: 149.2509 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 : 0.435 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3851 r_free = 0.3851 target = 0.166396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121108 restraints weight = 15147.849| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.85 r_work: 0.3083 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14966 Z= 0.178 Angle : 0.578 6.456 20469 Z= 0.306 Chirality : 0.043 0.158 2298 Planarity : 0.005 0.057 2418 Dihedral : 14.750 92.952 2710 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.84 % Allowed : 11.57 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1638 helix: 1.12 (0.20), residues: 658 sheet: -0.60 (0.30), residues: 244 loop : 0.40 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.021 0.002 TYR B 681 PHE 0.014 0.002 PHE A 103 TRP 0.012 0.001 TRP B 332 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14958) covalent geometry : angle 0.57465 / 0.31 (20463) hydrogen bonds : bond 0.05007 / 3.71 ( 645) hydrogen bonds : angle 4.84405 / 3.59 ( 1789) metal coordination : bond 0.01356 / 1.75 ( 8) metal coordination : angle 3.82790 / 7.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: A 200 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 219 SER cc_start: 0.8909 (t) cc_final: 0.8637 (p) REVERT: A 290 GLN cc_start: 0.8211 (mt0) cc_final: 0.7996 (mp10) REVERT: A 385 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8077 (mmtm) REVERT: A 453 GLU cc_start: 0.8055 (tt0) cc_final: 0.7692 (tp30) REVERT: A 482 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6346 (tm-30) REVERT: A 725 GLU cc_start: 0.7869 (tp30) cc_final: 0.7568 (tp30) REVERT: A 729 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7957 (mtt90) REVERT: A 848 HIS cc_start: 0.8151 (m-70) cc_final: 0.7637 (m90) REVERT: B 11 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 38 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: B 262 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7506 (ptpt) REVERT: B 410 GLU cc_start: 0.7445 (mp0) cc_final: 0.7245 (mp0) REVERT: B 428 ASN cc_start: 0.8671 (m-40) cc_final: 0.8327 (m-40) REVERT: B 479 GLN cc_start: 0.8338 (tp40) cc_final: 0.7569 (mp10) REVERT: B 594 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: B 608 MET cc_start: 0.8697 (mmt) cc_final: 0.8481 (mmt) REVERT: B 617 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7629 (ptm160) REVERT: B 626 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6952 (mmp80) REVERT: B 794 ASP cc_start: 0.7211 (t70) cc_final: 0.6769 (t0) REVERT: B 825 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: B 837 GLN cc_start: 0.7564 (tp40) cc_final: 0.7015 (tt0) outliers start: 42 outliers final: 12 residues processed: 227 average time/residue: 0.6729 time to fit residues: 165.2299 Evaluate side-chains 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 385 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 584 ILE 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 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 452 GLN Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 626 ARG Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 825 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 195 GLN B 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122052 restraints weight = 15312.115| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.78 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14966 Z= 0.148 Angle : 0.524 5.898 20469 Z= 0.279 Chirality : 0.041 0.153 2298 Planarity : 0.005 0.052 2418 Dihedral : 14.583 87.904 2709 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.64 % Allowed : 12.79 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1638 helix: 1.22 (0.20), residues: 656 sheet: -0.70 (0.31), residues: 244 loop : 0.45 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 414 TYR 0.019 0.001 TYR B 681 PHE 0.015 0.001 PHE A 103 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14958) covalent geometry : angle 0.52118 / 0.28 (20463) hydrogen bonds : bond 0.04662 / 3.45 ( 645) hydrogen bonds : angle 4.64463 / 3.43 ( 1789) metal coordination : bond 0.01344 / 1.72 ( 8) metal coordination : angle 3.35674 / 7.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: A 200 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: A 219 SER cc_start: 0.8900 (t) cc_final: 0.8674 (p) REVERT: A 290 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 351 MET cc_start: 0.8976 (mmm) cc_final: 0.8594 (mmm) REVERT: A 453 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 482 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6355 (tm-30) REVERT: A 485 ASP cc_start: 0.8659 (t70) cc_final: 0.8364 (t0) REVERT: A 649 GLU cc_start: 0.7916 (mp0) cc_final: 0.7523 (mp0) REVERT: A 729 ARG cc_start: 0.8243 (mtt90) cc_final: 0.8014 (mtt90) REVERT: A 830 MET cc_start: 0.7493 (tpp) cc_final: 0.6921 (mmm) REVERT: A 848 HIS cc_start: 0.8105 (m-70) cc_final: 0.7641 (m90) REVERT: B 11 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: B 38 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7808 (tp40) REVERT: B 428 ASN cc_start: 0.8718 (m-40) cc_final: 0.8338 (m-40) REVERT: B 479 GLN cc_start: 0.8360 (tp40) cc_final: 0.7537 (mp10) REVERT: B 594 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: B 608 MET cc_start: 0.8696 (mmt) cc_final: 0.8460 (mmt) REVERT: B 617 ARG cc_start: 0.7898 (ptm160) cc_final: 0.7572 (ptm160) REVERT: B 794 ASP cc_start: 0.7297 (t70) cc_final: 0.6885 (t0) REVERT: B 808 ASP cc_start: 0.8602 (m-30) cc_final: 0.8228 (m-30) REVERT: B 837 GLN cc_start: 0.7532 (tp40) cc_final: 0.7149 (tt0) outliers start: 39 outliers final: 14 residues processed: 220 average time/residue: 0.7278 time to fit residues: 173.6911 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 453 GLU 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 38 GLN Chi-restraints excluded: chain B residue 145 SER 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 776 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 844 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 276 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 = 0.3832 r_free = 0.3832 target = 0.164631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119620 restraints weight = 15242.860| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.77 r_work: 0.3054 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14966 Z= 0.239 Angle : 0.582 5.742 20469 Z= 0.304 Chirality : 0.043 0.148 2298 Planarity : 0.005 0.065 2418 Dihedral : 14.527 85.276 2702 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1638 helix: 1.06 (0.20), residues: 658 sheet: -0.72 (0.31), residues: 244 loop : 0.31 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 414 TYR 0.024 0.002 TYR B 681 PHE 0.016 0.002 PHE A 620 TRP 0.015 0.002 TRP B 332 HIS 0.010 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (14958) covalent geometry : angle 0.58013 / 0.30 (20463) hydrogen bonds : bond 0.04976 / 3.69 ( 645) hydrogen bonds : angle 4.67199 / 3.47 ( 1789) metal coordination : bond 0.01004 / 1.37 ( 8) metal coordination : angle 3.11450 / 6.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 200 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: A 290 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: A 335 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 414 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6892 (mtm110) REVERT: A 431 MET cc_start: 0.8876 (mmt) cc_final: 0.8455 (mmt) REVERT: A 453 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 482 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6303 (tm-30) REVERT: A 697 ILE cc_start: 0.8891 (mm) cc_final: 0.8687 (mp) REVERT: A 729 ARG cc_start: 0.8227 (mtt90) cc_final: 0.8005 (mtt90) REVERT: A 830 MET cc_start: 0.7494 (tpp) cc_final: 0.6779 (mmm) REVERT: A 848 HIS cc_start: 0.8145 (m-70) cc_final: 0.7550 (m-70) REVERT: B 11 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 38 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7850 (tp40) REVERT: B 428 ASN cc_start: 0.8752 (m-40) cc_final: 0.8302 (m-40) REVERT: B 479 GLN cc_start: 0.8341 (tp40) cc_final: 0.7530 (mp10) REVERT: B 594 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 608 MET cc_start: 0.8723 (mmt) cc_final: 0.8503 (mmt) REVERT: B 617 ARG cc_start: 0.7964 (ptm160) cc_final: 0.7556 (ptm160) REVERT: B 626 ARG cc_start: 0.7260 (mmp80) cc_final: 0.7038 (mmt180) REVERT: B 794 ASP cc_start: 0.7287 (t70) cc_final: 0.6862 (t0) REVERT: B 808 ASP cc_start: 0.8641 (m-30) cc_final: 0.8329 (m-30) REVERT: B 837 GLN cc_start: 0.7633 (tp40) cc_final: 0.7229 (tt0) outliers start: 41 outliers final: 16 residues processed: 215 average time/residue: 0.7288 time to fit residues: 170.0811 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 453 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 101 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 420 HIS 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 = 0.3849 r_free = 0.3849 target = 0.166234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119894 restraints weight = 15192.892| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.89 r_work: 0.3054 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14966 Z= 0.154 Angle : 0.525 6.391 20469 Z= 0.276 Chirality : 0.041 0.150 2298 Planarity : 0.005 0.056 2418 Dihedral : 14.464 85.179 2702 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.98 % Allowed : 14.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1638 helix: 1.20 (0.20), residues: 658 sheet: -0.74 (0.32), residues: 236 loop : 0.36 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 689 TYR 0.023 0.001 TYR B 681 PHE 0.010 0.001 PHE B 151 TRP 0.011 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (14958) covalent geometry : angle 0.52277 / 0.28 (20463) hydrogen bonds : bond 0.04568 / 3.38 ( 645) hydrogen bonds : angle 4.59412 / 3.39 ( 1789) metal coordination : bond 0.01174 / 1.58 ( 8) metal coordination : angle 3.05815 / 6.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: A 200 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: A 265 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 337 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8709 (ptmm) REVERT: A 351 MET cc_start: 0.9003 (mmm) cc_final: 0.8639 (mmm) REVERT: A 385 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8105 (mmtm) REVERT: A 431 MET cc_start: 0.8870 (mmt) cc_final: 0.8363 (mmp) REVERT: A 453 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 482 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6230 (tm-30) REVERT: A 485 ASP cc_start: 0.8769 (t70) cc_final: 0.8499 (t0) REVERT: A 533 MET cc_start: 0.8067 (ttm) cc_final: 0.7866 (tpp) REVERT: A 649 GLU cc_start: 0.7958 (mp0) cc_final: 0.7506 (mp0) REVERT: A 697 ILE cc_start: 0.8951 (mm) cc_final: 0.8750 (mp) REVERT: A 729 ARG cc_start: 0.8265 (mtt90) cc_final: 0.8021 (mtt90) REVERT: A 818 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: A 830 MET cc_start: 0.7473 (tpp) cc_final: 0.6781 (mmm) REVERT: A 848 HIS cc_start: 0.8192 (m-70) cc_final: 0.7552 (m-70) REVERT: B 11 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 38 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7855 (tp40) REVERT: B 350 MET cc_start: 0.9115 (mtp) cc_final: 0.8876 (mtt) REVERT: B 428 ASN cc_start: 0.8789 (m-40) cc_final: 0.8353 (m-40) REVERT: B 479 GLN cc_start: 0.8319 (tp40) cc_final: 0.7514 (mp10) REVERT: B 594 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 617 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7532 (ptm160) REVERT: B 794 ASP cc_start: 0.7258 (t70) cc_final: 0.6834 (t0) REVERT: B 808 ASP cc_start: 0.8631 (m-30) cc_final: 0.8319 (m-30) outliers start: 44 outliers final: 20 residues processed: 216 average time/residue: 0.7146 time to fit residues: 167.7310 Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 881 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 168 optimal weight: 10.9990 chunk 165 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 545 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 = 0.3842 r_free = 0.3842 target = 0.165511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119081 restraints weight = 15212.645| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.89 r_work: 0.3028 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14966 Z= 0.192 Angle : 0.545 6.520 20469 Z= 0.285 Chirality : 0.041 0.148 2298 Planarity : 0.005 0.079 2418 Dihedral : 14.437 84.991 2702 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.38 % Allowed : 14.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1638 helix: 1.17 (0.20), residues: 658 sheet: -0.73 (0.32), residues: 236 loop : 0.31 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 414 TYR 0.025 0.002 TYR B 681 PHE 0.012 0.001 PHE B 151 TRP 0.012 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (14958) covalent geometry : angle 0.54282 / 0.29 (20463) hydrogen bonds : bond 0.04664 / 3.45 ( 645) hydrogen bonds : angle 4.61305 / 3.41 ( 1789) metal coordination : bond 0.01020 / 1.44 ( 8) metal coordination : angle 2.81242 / 6.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: A 102 CYS cc_start: 0.8506 (t) cc_final: 0.8149 (m) REVERT: A 200 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: A 265 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 335 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: A 337 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8716 (ptmm) REVERT: A 351 MET cc_start: 0.9007 (mmm) cc_final: 0.8470 (mmm) REVERT: A 385 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (mmtm) REVERT: A 414 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6816 (mtm110) REVERT: A 453 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: A 482 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6189 (tm-30) REVERT: A 533 MET cc_start: 0.8050 (ttm) cc_final: 0.7753 (tpp) REVERT: A 649 GLU cc_start: 0.7971 (mp0) cc_final: 0.7621 (mp0) REVERT: A 729 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7806 (mtt90) REVERT: A 818 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: A 830 MET cc_start: 0.7452 (tpp) cc_final: 0.6769 (mmm) REVERT: A 848 HIS cc_start: 0.8195 (m-70) cc_final: 0.7550 (m-70) REVERT: B 11 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: B 38 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: B 229 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7057 (ptp-110) REVERT: B 428 ASN cc_start: 0.8784 (m-40) cc_final: 0.8332 (m-40) REVERT: B 479 GLN cc_start: 0.8314 (tp40) cc_final: 0.7493 (mp10) REVERT: B 594 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 605 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: B 617 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7517 (ptm160) REVERT: B 626 ARG cc_start: 0.7203 (mmp-170) cc_final: 0.6976 (mmp-170) REVERT: B 637 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7560 (ptm-80) REVERT: B 794 ASP cc_start: 0.7205 (t70) cc_final: 0.6744 (t0) REVERT: B 808 ASP cc_start: 0.8630 (m-30) cc_final: 0.8269 (m-30) REVERT: B 837 GLN cc_start: 0.7750 (tp40) cc_final: 0.7279 (tt0) outliers start: 50 outliers final: 21 residues processed: 217 average time/residue: 0.6891 time to fit residues: 162.7702 Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 73 MET Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 818 GLU 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 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 637 ARG 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 41 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 545 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 = 0.3847 r_free = 0.3847 target = 0.165984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121087 restraints weight = 15119.021| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.76 r_work: 0.3079 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14966 Z= 0.161 Angle : 0.528 6.788 20469 Z= 0.277 Chirality : 0.041 0.148 2298 Planarity : 0.005 0.063 2418 Dihedral : 14.407 84.904 2702 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.84 % Allowed : 15.22 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1638 helix: 1.21 (0.20), residues: 658 sheet: -0.72 (0.31), residues: 244 loop : 0.28 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 689 TYR 0.016 0.001 TYR A 234 PHE 0.020 0.001 PHE A 620 TRP 0.011 0.001 TRP B 332 HIS 0.006 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (14958) covalent geometry : angle 0.52561 / 0.28 (20463) hydrogen bonds : bond 0.04525 / 3.34 ( 645) hydrogen bonds : angle 4.56562 / 3.37 ( 1789) metal coordination : bond 0.01047 / 1.46 ( 8) metal coordination : angle 2.83552 / 6.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 102 CYS cc_start: 0.8466 (t) cc_final: 0.8114 (m) REVERT: A 200 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: A 265 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 335 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: A 351 MET cc_start: 0.8928 (mmm) cc_final: 0.8412 (mmm) REVERT: A 385 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (mmtm) REVERT: A 414 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6660 (ttp-110) REVERT: A 431 MET cc_start: 0.8845 (mmt) cc_final: 0.8326 (mmp) REVERT: A 482 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6074 (tm-30) REVERT: A 485 ASP cc_start: 0.8692 (t70) cc_final: 0.8402 (t0) REVERT: A 533 MET cc_start: 0.8012 (ttm) cc_final: 0.7727 (tpp) REVERT: A 649 GLU cc_start: 0.7900 (mp0) cc_final: 0.7537 (mp0) REVERT: A 729 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7727 (mtt90) REVERT: A 818 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: A 830 MET cc_start: 0.7505 (tpp) cc_final: 0.6861 (mmm) REVERT: A 848 HIS cc_start: 0.8151 (m-70) cc_final: 0.7643 (m90) REVERT: B 11 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: B 38 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7815 (tp40) REVERT: B 273 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8247 (tttp) REVERT: B 301 ASN cc_start: 0.7932 (m-40) cc_final: 0.7195 (m-40) REVERT: B 350 MET cc_start: 0.9062 (mtp) cc_final: 0.8809 (mtt) REVERT: B 428 ASN cc_start: 0.8775 (m-40) cc_final: 0.8354 (m-40) REVERT: B 479 GLN cc_start: 0.8312 (tp40) cc_final: 0.7522 (mp10) REVERT: B 594 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 605 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (ttpp) REVERT: B 617 ARG cc_start: 0.7953 (ptm160) cc_final: 0.7456 (ptm160) REVERT: B 637 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7517 (ptm-80) REVERT: B 690 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6480 (mtt90) REVERT: B 794 ASP cc_start: 0.7214 (t70) cc_final: 0.6780 (t0) REVERT: B 808 ASP cc_start: 0.8576 (m-30) cc_final: 0.8223 (m-30) outliers start: 42 outliers final: 22 residues processed: 211 average time/residue: 0.7208 time to fit residues: 165.3977 Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 73 MET Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 881 VAL 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 229 ARG 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 605 LYS Chi-restraints excluded: chain B residue 637 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 156 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 545 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 = 0.3871 r_free = 0.3871 target = 0.168187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123482 restraints weight = 15183.234| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.78 r_work: 0.3161 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14966 Z= 0.118 Angle : 0.500 7.034 20469 Z= 0.263 Chirality : 0.039 0.150 2298 Planarity : 0.005 0.063 2418 Dihedral : 14.321 84.644 2702 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.50 % Allowed : 15.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1638 helix: 1.42 (0.20), residues: 658 sheet: -0.66 (0.32), residues: 238 loop : 0.31 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 689 TYR 0.023 0.001 TYR B 681 PHE 0.011 0.001 PHE B 435 TRP 0.009 0.001 TRP B 413 HIS 0.006 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14958) covalent geometry : angle 0.49801 / 0.26 (20463) hydrogen bonds : bond 0.04196 / 3.10 ( 645) hydrogen bonds : angle 4.44805 / 3.27 ( 1789) metal coordination : bond 0.01096 / 1.41 ( 8) metal coordination : angle 2.75966 / 5.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: A 102 CYS cc_start: 0.8531 (t) cc_final: 0.8128 (m) REVERT: A 200 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: A 351 MET cc_start: 0.8999 (mmm) cc_final: 0.8722 (mmm) REVERT: A 385 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8090 (mmtm) REVERT: A 414 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6657 (ptt-90) REVERT: A 431 MET cc_start: 0.8819 (mmt) cc_final: 0.8349 (mmp) REVERT: A 482 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6121 (tm-30) REVERT: A 485 ASP cc_start: 0.8670 (t70) cc_final: 0.8395 (t0) REVERT: A 729 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7761 (mtt90) REVERT: A 818 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: A 830 MET cc_start: 0.7426 (tpp) cc_final: 0.6798 (mmm) REVERT: A 848 HIS cc_start: 0.8181 (m-70) cc_final: 0.7523 (m-70) REVERT: B 11 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 301 ASN cc_start: 0.7956 (m-40) cc_final: 0.6934 (t0) REVERT: B 428 ASN cc_start: 0.8777 (m-40) cc_final: 0.8421 (m-40) REVERT: B 479 GLN cc_start: 0.8291 (tp40) cc_final: 0.7493 (mp10) REVERT: B 617 ARG cc_start: 0.8005 (ptm160) cc_final: 0.7509 (ptm160) REVERT: B 690 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6326 (mtt90) REVERT: B 794 ASP cc_start: 0.7346 (t70) cc_final: 0.6921 (t0) REVERT: B 808 ASP cc_start: 0.8562 (m-30) cc_final: 0.8169 (m-30) outliers start: 37 outliers final: 15 residues processed: 214 average time/residue: 0.7026 time to fit residues: 163.7854 Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER 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 818 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3874 r_free = 0.3874 target = 0.168474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124102 restraints weight = 15225.084| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.76 r_work: 0.3127 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14966 Z= 0.120 Angle : 0.505 7.138 20469 Z= 0.265 Chirality : 0.039 0.150 2298 Planarity : 0.005 0.058 2418 Dihedral : 14.286 84.019 2702 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.56 % Allowed : 16.91 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1638 helix: 1.49 (0.20), residues: 660 sheet: -0.51 (0.32), residues: 246 loop : 0.30 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 689 TYR 0.023 0.001 TYR B 681 PHE 0.012 0.001 PHE B 435 TRP 0.007 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14958) covalent geometry : angle 0.50346 / 0.26 (20463) hydrogen bonds : bond 0.04137 / 3.06 ( 645) hydrogen bonds : angle 4.40645 / 3.23 ( 1789) metal coordination : bond 0.01123 / 1.50 ( 8) metal coordination : angle 2.54591 / 5.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: A 102 CYS cc_start: 0.8527 (t) cc_final: 0.8155 (m) REVERT: A 265 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7920 (m) REVERT: A 335 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: A 351 MET cc_start: 0.9001 (mmm) cc_final: 0.8656 (mmm) REVERT: A 385 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (mmtm) REVERT: A 414 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6748 (ptt-90) REVERT: A 482 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6155 (tm-30) REVERT: A 485 ASP cc_start: 0.8622 (t70) cc_final: 0.8367 (t0) REVERT: A 649 GLU cc_start: 0.7945 (mp0) cc_final: 0.7597 (mp0) REVERT: A 729 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7818 (mtt90) REVERT: A 830 MET cc_start: 0.7429 (tpp) cc_final: 0.6812 (mmm) REVERT: A 848 HIS cc_start: 0.8211 (m-70) cc_final: 0.7591 (m-70) REVERT: B 11 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: B 273 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8239 (tttp) REVERT: B 301 ASN cc_start: 0.7964 (m-40) cc_final: 0.7009 (t0) REVERT: B 428 ASN cc_start: 0.8781 (m-40) cc_final: 0.8471 (m-40) REVERT: B 479 GLN cc_start: 0.8295 (tp40) cc_final: 0.7454 (mp10) REVERT: B 617 ARG cc_start: 0.8021 (ptm160) cc_final: 0.7520 (ptm160) REVERT: B 690 ARG cc_start: 0.6629 (mtm110) cc_final: 0.6328 (mtt90) REVERT: B 794 ASP cc_start: 0.7388 (t70) cc_final: 0.6958 (t0) REVERT: B 808 ASP cc_start: 0.8572 (m-30) cc_final: 0.8219 (m-30) outliers start: 23 outliers final: 14 residues processed: 205 average time/residue: 0.6947 time to fit residues: 155.0635 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 748 ILE 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 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 675 THR Chi-restraints excluded: chain B residue 712 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3877 r_free = 0.3877 target = 0.168695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123116 restraints weight = 15269.101| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.88 r_work: 0.3120 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14966 Z= 0.119 Angle : 0.506 7.262 20469 Z= 0.265 Chirality : 0.040 0.174 2298 Planarity : 0.005 0.070 2418 Dihedral : 14.279 83.663 2702 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.89 % Allowed : 16.64 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1638 helix: 1.50 (0.20), residues: 660 sheet: -0.46 (0.32), residues: 246 loop : 0.30 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 689 TYR 0.024 0.001 TYR A 681 PHE 0.012 0.001 PHE B 435 TRP 0.008 0.001 TRP B 413 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14958) covalent geometry : angle 0.50398 / 0.27 (20463) hydrogen bonds : bond 0.04116 / 3.04 ( 645) hydrogen bonds : angle 4.40157 / 3.22 ( 1789) metal coordination : bond 0.01118 / 1.47 ( 8) metal coordination : angle 2.51327 / 5.29 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 265 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.7969 (m) REVERT: A 335 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: A 351 MET cc_start: 0.9005 (mmm) cc_final: 0.8655 (mmm) REVERT: A 385 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8086 (mmtm) REVERT: A 414 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6716 (ptt-90) REVERT: A 482 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6170 (tm-30) REVERT: A 485 ASP cc_start: 0.8638 (t70) cc_final: 0.8360 (t0) REVERT: A 649 GLU cc_start: 0.7971 (mp0) cc_final: 0.7604 (mp0) REVERT: A 729 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7823 (mtt90) REVERT: A 818 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: A 830 MET cc_start: 0.7407 (tpp) cc_final: 0.6998 (mmm) REVERT: A 848 HIS cc_start: 0.8222 (m-70) cc_final: 0.7741 (m90) REVERT: B 11 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: B 119 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6333 (mtt90) REVERT: B 301 ASN cc_start: 0.7930 (m-40) cc_final: 0.7012 (t0) REVERT: B 428 ASN cc_start: 0.8755 (m-40) cc_final: 0.8430 (m-40) REVERT: B 479 GLN cc_start: 0.8327 (tp40) cc_final: 0.7431 (mp10) REVERT: B 594 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: B 617 ARG cc_start: 0.8001 (ptm160) cc_final: 0.7480 (ptm160) REVERT: B 690 ARG cc_start: 0.6627 (mtm110) cc_final: 0.6289 (mtt90) REVERT: B 794 ASP cc_start: 0.7329 (t70) cc_final: 0.6887 (t0) REVERT: B 808 ASP cc_start: 0.8601 (m-30) cc_final: 0.8257 (m-30) outliers start: 28 outliers final: 16 residues processed: 199 average time/residue: 0.6909 time to fit residues: 149.7601 Evaluate side-chains 201 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 145 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3867 r_free = 0.3867 target = 0.167775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123589 restraints weight = 15124.673| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.74 r_work: 0.3104 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14966 Z= 0.155 Angle : 0.521 7.052 20469 Z= 0.272 Chirality : 0.040 0.148 2298 Planarity : 0.005 0.069 2418 Dihedral : 14.291 83.255 2702 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 16.71 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1638 helix: 1.44 (0.20), residues: 660 sheet: -0.42 (0.32), residues: 244 loop : 0.30 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 689 TYR 0.025 0.002 TYR B 681 PHE 0.011 0.001 PHE B 435 TRP 0.009 0.001 TRP B 332 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14958) covalent geometry : angle 0.51913 / 0.27 (20463) hydrogen bonds : bond 0.04258 / 3.14 ( 645) hydrogen bonds : angle 4.43363 / 3.26 ( 1789) metal coordination : bond 0.00926 / 1.29 ( 8) metal coordination : angle 2.51381 / 5.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.95 seconds wall clock time: 94 minutes 45.97 seconds (5685.97 seconds total)