Starting phenix.real_space_refine on Fri Jul 3 13:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ere_19913/07_2026/9ere_19913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ere_19913/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ere_19913/07_2026/9ere_19913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ere_19913/07_2026/9ere_19913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ere_19913/07_2026/9ere_19913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ere_19913/07_2026/9ere_19913.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 1 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 2.30, per 1000 atoms: 0.16 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: 1.10 Conformation dependent library (CDL) restraints added in 455.0 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: 1.70 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: 2.06 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2226 1.28 - 1.41: 3908 1.41 - 1.55: 8591 1.55 - 1.68: 111 1.68 - 1.81: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ARG B 729 " pdb=" C ARG B 729 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.24e-02 6.50e+03 7.03e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.234 1.148 0.087 1.26e-02 6.30e+03 4.72e+01 bond pdb=" C ARG A 862 " pdb=" O ARG A 862 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.22e-02 6.72e+03 3.04e+01 bond pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.82e+01 bond pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.21e-02 6.83e+03 2.35e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19984 1.78 - 3.56: 398 3.56 - 5.35: 68 5.35 - 7.13: 10 7.13 - 8.91: 3 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.71 120.44 -8.73 1.15e+00 7.56e-01 5.77e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 111.28 117.35 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" C GLN A 774 " ideal model delta sigma weight residual 110.20 118.26 -8.06 1.58e+00 4.01e-01 2.60e+01 angle pdb=" C PRO A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.84 113.57 6.27 1.25e+00 6.40e-01 2.51e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8229 19.09 - 38.18: 626 38.18 - 57.26: 221 57.26 - 76.35: 105 76.35 - 95.44: 18 Dihedral angle restraints: 9199 sinusoidal: 4367 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 136.56 95.44 1 1.70e+01 3.46e-03 3.64e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C ARG B 729 " pdb=" N ARG B 729 " pdb=" CA ARG B 729 " pdb=" CB ARG B 729 " ideal model delta harmonic sigma weight residual -122.60 -112.06 -10.54 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2067 0.067 - 0.134: 221 0.134 - 0.202: 6 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA LEU B 636 " pdb=" N LEU B 636 " pdb=" C LEU B 636 " pdb=" CB LEU B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN A 706 " pdb=" N GLN A 706 " pdb=" C GLN A 706 " pdb=" CB GLN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 705 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 705 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE A 705 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 706 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 851 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LEU A 851 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 851 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 852 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C THR B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O THR B 728 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 729 " -0.018 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 10482 3.10 - 3.70: 23246 3.70 - 4.30: 35303 4.30 - 4.90: 57539 Nonbonded interactions: 126660 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 1.903 3.060 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 3.060 nonbonded pdb=" OE2 GLU A 209 " pdb="MN MN A1002 " model vdw 2.051 3.060 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 2.062 3.060 ... (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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- 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= 0.274 Angle : 0.644 8.911 20469 Z= 0.399 Chirality : 0.042 0.336 2298 Planarity : 0.006 0.084 2418 Dihedral : 17.120 95.438 6075 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.61 % Allowed : 11.91 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 0.00488 / 0.27 (14958) covalent geometry : angle 0.64060 / 0.40 (20463) hydrogen bonds : bond 0.12258 / 9.08 ( 645) hydrogen bonds : angle 5.74508 / 4.18 ( 1789) metal coordination : bond 0.01942 / 1.26 ( 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 : 0.579 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: 0.6328 time to fit residues: 147.9083 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 : 0.430 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120182 restraints weight = 15152.711| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.90 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14966 Z= 0.182 Angle : 0.573 6.892 20469 Z= 0.304 Chirality : 0.042 0.156 2298 Planarity : 0.005 0.048 2418 Dihedral : 14.875 92.618 2710 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.84 % Allowed : 11.84 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.21), residues: 1638 helix: 1.14 (0.20), residues: 658 sheet: -0.57 (0.30), residues: 244 loop : 0.41 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 617 TYR 0.021 0.002 TYR B 681 PHE 0.013 0.002 PHE A 103 TRP 0.012 0.001 TRP B 332 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (14958) covalent geometry : angle 0.56913 / 0.30 (20463) hydrogen bonds : bond 0.05116 / 3.73 ( 645) hydrogen bonds : angle 4.88665 / 3.61 ( 1789) metal coordination : bond 0.01397 / 0.89 ( 8) metal coordination : angle 3.98635 / 8.32 ( 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 241 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: A 200 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 219 SER cc_start: 0.8934 (t) cc_final: 0.8665 (p) REVERT: A 290 GLN cc_start: 0.8262 (mt0) cc_final: 0.8005 (mp10) REVERT: A 385 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (mmtm) REVERT: A 453 GLU cc_start: 0.8083 (tt0) cc_final: 0.7708 (tp30) REVERT: A 482 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 649 GLU cc_start: 0.8111 (mp0) cc_final: 0.7612 (mp0) REVERT: A 729 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7994 (mtt90) REVERT: A 848 HIS cc_start: 0.8194 (m-70) cc_final: 0.7659 (m90) REVERT: B 11 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: B 428 ASN cc_start: 0.8589 (m-40) cc_final: 0.8221 (m-40) REVERT: B 479 GLN cc_start: 0.8345 (tp40) cc_final: 0.7577 (mp10) REVERT: B 594 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: B 617 ARG cc_start: 0.7911 (ptm160) cc_final: 0.7701 (ptm160) REVERT: B 677 ASP cc_start: 0.7713 (t0) cc_final: 0.7497 (t0) REVERT: B 794 ASP cc_start: 0.7247 (t70) cc_final: 0.6810 (t0) outliers start: 42 outliers final: 12 residues processed: 225 average time/residue: 0.5995 time to fit residues: 146.3050 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN A 661 HIS B 195 GLN B 224 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 = 0.3846 r_free = 0.3846 target = 0.166058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119657 restraints weight = 15325.690| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.90 r_work: 0.3072 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1106 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= 0.188 Angle : 0.552 6.187 20469 Z= 0.292 Chirality : 0.042 0.148 2298 Planarity : 0.005 0.051 2418 Dihedral : 14.726 89.271 2709 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.91 % Allowed : 12.99 % Favored : 84.10 % 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: 1.15 (0.20), residues: 656 sheet: -0.77 (0.30), residues: 246 loop : 0.44 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 414 TYR 0.020 0.002 TYR B 681 PHE 0.011 0.001 PHE A 435 TRP 0.013 0.001 TRP B 332 HIS 0.010 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (14958) covalent geometry : angle 0.54881 / 0.29 (20463) hydrogen bonds : bond 0.04817 / 3.51 ( 645) hydrogen bonds : angle 4.72624 / 3.49 ( 1789) metal coordination : bond 0.01222 / 0.80 ( 8) metal coordination : angle 3.43619 / 7.35 ( 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 242 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 102 CYS cc_start: 0.8682 (t) cc_final: 0.8176 (m) REVERT: A 200 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: A 219 SER cc_start: 0.8952 (t) cc_final: 0.8723 (p) REVERT: A 290 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: A 335 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: A 453 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: A 482 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6390 (tm-30) REVERT: A 485 ASP cc_start: 0.8712 (t70) cc_final: 0.8410 (t0) REVERT: A 649 GLU cc_start: 0.7986 (mp0) cc_final: 0.7591 (mp0) REVERT: A 725 GLU cc_start: 0.7883 (tp30) cc_final: 0.7645 (tp30) REVERT: A 729 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8036 (mtt90) REVERT: A 830 MET cc_start: 0.7469 (tpp) cc_final: 0.6873 (mmm) REVERT: A 848 HIS cc_start: 0.8192 (m-70) cc_final: 0.7696 (m90) REVERT: B 11 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: B 38 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (tp40) REVERT: B 233 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: B 428 ASN cc_start: 0.8756 (m-40) cc_final: 0.8366 (m-40) REVERT: B 479 GLN cc_start: 0.8364 (tp40) cc_final: 0.7551 (mp10) REVERT: B 594 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 608 MET cc_start: 0.8728 (mmt) cc_final: 0.8508 (mmt) REVERT: B 617 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7557 (ptm160) REVERT: B 677 ASP cc_start: 0.7821 (t0) cc_final: 0.7568 (t0) REVERT: B 794 ASP cc_start: 0.7307 (t70) cc_final: 0.6865 (t0) REVERT: B 808 ASP cc_start: 0.8641 (m-30) cc_final: 0.8290 (m-30) REVERT: B 837 GLN cc_start: 0.7595 (tp40) cc_final: 0.7125 (tt0) outliers start: 43 outliers final: 18 residues processed: 221 average time/residue: 0.5592 time to fit residues: 134.2902 Evaluate side-chains 218 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 418 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain 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 233 GLU 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 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 844 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 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: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 224 GLN B 276 GLN B 420 HIS B 848 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120694 restraints weight = 15237.685| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.78 r_work: 0.3065 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14966 Z= 0.190 Angle : 0.547 5.962 20469 Z= 0.288 Chirality : 0.042 0.147 2298 Planarity : 0.005 0.054 2418 Dihedral : 14.645 86.060 2709 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.18 % Allowed : 13.13 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1638 helix: 1.16 (0.20), residues: 658 sheet: -0.80 (0.31), residues: 238 loop : 0.41 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 414 TYR 0.022 0.002 TYR B 681 PHE 0.013 0.002 PHE A 620 TRP 0.012 0.002 TRP B 332 HIS 0.012 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (14958) covalent geometry : angle 0.54397 / 0.29 (20463) hydrogen bonds : bond 0.04689 / 3.42 ( 645) hydrogen bonds : angle 4.66148 / 3.44 ( 1789) metal coordination : bond 0.01126 / 0.74 ( 8) metal coordination : angle 3.22490 / 6.98 ( 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 242 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: A 102 CYS cc_start: 0.8635 (t) cc_final: 0.8155 (m) REVERT: A 200 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: A 219 SER cc_start: 0.8909 (t) cc_final: 0.8695 (p) REVERT: A 290 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: A 335 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: A 385 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8098 (mmtm) REVERT: A 414 ARG cc_start: 0.7282 (mtm110) cc_final: 0.6991 (mtm110) REVERT: A 453 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 482 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6340 (tm-30) REVERT: A 485 ASP cc_start: 0.8635 (t70) cc_final: 0.8330 (t0) REVERT: A 533 MET cc_start: 0.7974 (ttm) cc_final: 0.7752 (tpp) REVERT: A 649 GLU cc_start: 0.7856 (mp0) cc_final: 0.7431 (mp0) REVERT: A 697 ILE cc_start: 0.8856 (mm) cc_final: 0.8637 (mp) REVERT: A 729 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7943 (mtt90) REVERT: A 830 MET cc_start: 0.7488 (tpp) cc_final: 0.6773 (mmm) REVERT: A 848 HIS cc_start: 0.8109 (m-70) cc_final: 0.7606 (m90) REVERT: B 11 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: B 38 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7813 (tp40) REVERT: B 229 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.6619 (ptt-90) REVERT: B 428 ASN cc_start: 0.8739 (m-40) cc_final: 0.8293 (m-40) REVERT: B 479 GLN cc_start: 0.8345 (tp40) cc_final: 0.7550 (mp10) REVERT: B 594 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 608 MET cc_start: 0.8691 (mmt) cc_final: 0.8476 (mmt) REVERT: B 617 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7542 (ptm160) REVERT: B 677 ASP cc_start: 0.7800 (t0) cc_final: 0.7549 (t0) REVERT: B 794 ASP cc_start: 0.7254 (t70) cc_final: 0.6810 (t0) REVERT: B 808 ASP cc_start: 0.8608 (m-30) cc_final: 0.8304 (m-30) REVERT: B 837 GLN cc_start: 0.7516 (tp40) cc_final: 0.7134 (tt0) outliers start: 47 outliers final: 20 residues processed: 223 average time/residue: 0.5741 time to fit residues: 139.6325 Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 290 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ASP 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 584 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 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 626 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.166980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122053 restraints weight = 15161.821| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.77 r_work: 0.3087 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14966 Z= 0.150 Angle : 0.515 6.109 20469 Z= 0.272 Chirality : 0.041 0.150 2298 Planarity : 0.005 0.057 2418 Dihedral : 14.549 85.914 2705 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 14.34 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1638 helix: 1.27 (0.20), residues: 658 sheet: -0.79 (0.32), residues: 238 loop : 0.41 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 689 TYR 0.024 0.001 TYR B 681 PHE 0.010 0.001 PHE B 151 TRP 0.010 0.001 TRP B 332 HIS 0.010 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14958) covalent geometry : angle 0.51280 / 0.27 (20463) hydrogen bonds : bond 0.04460 / 3.24 ( 645) hydrogen bonds : angle 4.58356 / 3.37 ( 1789) metal coordination : bond 0.01167 / 0.75 ( 8) metal coordination : angle 3.00837 / 6.41 ( 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 233 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: A 102 CYS cc_start: 0.8640 (t) cc_final: 0.8175 (m) REVERT: A 200 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: A 335 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: A 337 LYS cc_start: 0.8900 (ptpt) cc_final: 0.8696 (ptmm) REVERT: A 385 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (mmtm) REVERT: A 431 MET cc_start: 0.8835 (mmt) cc_final: 0.8325 (mmp) REVERT: A 453 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: A 482 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6195 (tm-30) REVERT: A 485 ASP cc_start: 0.8620 (t70) cc_final: 0.8342 (t0) REVERT: A 649 GLU cc_start: 0.7884 (mp0) cc_final: 0.7439 (mp0) REVERT: A 729 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7963 (mtt90) REVERT: A 830 MET cc_start: 0.7473 (tpp) cc_final: 0.6770 (mmm) REVERT: A 848 HIS cc_start: 0.8144 (m-70) cc_final: 0.7507 (m-70) REVERT: B 11 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 38 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: B 428 ASN cc_start: 0.8764 (m-40) cc_final: 0.8357 (m-40) REVERT: B 479 GLN cc_start: 0.8344 (tp40) cc_final: 0.7552 (mp10) REVERT: B 594 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: B 617 ARG cc_start: 0.7948 (ptm160) cc_final: 0.7495 (ptm160) REVERT: B 637 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7515 (ptm-80) REVERT: B 677 ASP cc_start: 0.7705 (t0) cc_final: 0.7421 (t0) REVERT: B 794 ASP cc_start: 0.7219 (t70) cc_final: 0.6800 (t0) REVERT: B 808 ASP cc_start: 0.8590 (m-30) cc_final: 0.8244 (m-30) outliers start: 40 outliers final: 14 residues processed: 215 average time/residue: 0.5510 time to fit residues: 129.3369 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 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 637 ARG Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.166629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121052 restraints weight = 15173.914| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.86 r_work: 0.3134 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1529 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= 0.163 Angle : 0.527 7.566 20469 Z= 0.276 Chirality : 0.041 0.147 2298 Planarity : 0.005 0.080 2418 Dihedral : 14.505 85.773 2702 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.18 % Allowed : 14.82 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.21), residues: 1638 helix: 1.24 (0.20), residues: 660 sheet: -0.78 (0.32), residues: 238 loop : 0.36 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 414 TYR 0.024 0.001 TYR B 681 PHE 0.015 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 0.00385 / 0.16 (14958) covalent geometry : angle 0.52519 / 0.28 (20463) hydrogen bonds : bond 0.04481 / 3.26 ( 645) hydrogen bonds : angle 4.56912 / 3.35 ( 1789) metal coordination : bond 0.01033 / 0.69 ( 8) metal coordination : angle 2.73314 / 6.01 ( 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 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 102 CYS cc_start: 0.8625 (t) cc_final: 0.8195 (m) REVERT: A 200 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: A 265 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 335 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: A 385 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8160 (mmtm) REVERT: A 414 ARG cc_start: 0.7266 (mtm110) cc_final: 0.6913 (mtm110) REVERT: A 431 MET cc_start: 0.8876 (mmt) cc_final: 0.8365 (mmp) REVERT: A 482 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6209 (tm-30) REVERT: A 485 ASP cc_start: 0.8676 (t70) cc_final: 0.8408 (t0) REVERT: A 649 GLU cc_start: 0.7983 (mp0) cc_final: 0.7654 (mp0) REVERT: A 729 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7802 (mtt90) REVERT: A 830 MET cc_start: 0.7462 (tpp) cc_final: 0.6767 (mmm) REVERT: A 848 HIS cc_start: 0.8214 (m-70) cc_final: 0.7592 (m-70) REVERT: B 11 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 38 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7910 (tp40) REVERT: B 262 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7501 (ptpt) REVERT: B 428 ASN cc_start: 0.8799 (m-40) cc_final: 0.8405 (m-40) REVERT: B 479 GLN cc_start: 0.8295 (tp40) cc_final: 0.7511 (mp10) REVERT: B 594 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: B 605 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8329 (ttpp) REVERT: B 617 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7522 (ptm160) REVERT: B 637 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7793 (ptm-80) REVERT: B 677 ASP cc_start: 0.7666 (t70) cc_final: 0.7406 (t0) REVERT: B 794 ASP cc_start: 0.7301 (t70) cc_final: 0.6877 (t0) REVERT: B 808 ASP cc_start: 0.8606 (m-30) cc_final: 0.8271 (m-30) outliers start: 47 outliers final: 19 residues processed: 215 average time/residue: 0.5661 time to fit residues: 132.9935 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.8980 chunk 10 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.166521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121500 restraints weight = 15093.116| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.76 r_work: 0.3100 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14966 Z= 0.174 Angle : 0.532 7.136 20469 Z= 0.279 Chirality : 0.041 0.147 2298 Planarity : 0.005 0.058 2418 Dihedral : 14.485 85.587 2702 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.64 % Allowed : 15.49 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1638 helix: 1.23 (0.20), residues: 658 sheet: -0.78 (0.32), residues: 238 loop : 0.32 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 689 TYR 0.016 0.002 TYR A 234 PHE 0.011 0.001 PHE B 151 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 0.00414 / 0.17 (14958) covalent geometry : angle 0.53043 / 0.28 (20463) hydrogen bonds : bond 0.04513 / 3.28 ( 645) hydrogen bonds : angle 4.56506 / 3.35 ( 1789) metal coordination : bond 0.00992 / 0.66 ( 8) metal coordination : angle 2.74930 / 5.95 ( 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 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 102 CYS cc_start: 0.8585 (t) cc_final: 0.8137 (m) REVERT: A 200 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: A 265 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 335 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: A 385 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (mmtm) REVERT: A 414 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6884 (mtm110) REVERT: A 431 MET cc_start: 0.8862 (mmt) cc_final: 0.8367 (mmp) REVERT: A 482 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6092 (tm-30) REVERT: A 485 ASP cc_start: 0.8626 (t70) cc_final: 0.8322 (t0) REVERT: A 649 GLU cc_start: 0.7897 (mp0) cc_final: 0.7546 (mp0) REVERT: A 729 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7787 (mtt90) REVERT: A 830 MET cc_start: 0.7454 (tpp) cc_final: 0.6761 (mmm) REVERT: A 848 HIS cc_start: 0.8158 (m-70) cc_final: 0.7516 (m-70) REVERT: B 11 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 38 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7818 (tp40) REVERT: B 301 ASN cc_start: 0.7907 (m-40) cc_final: 0.7183 (m-40) REVERT: B 428 ASN cc_start: 0.8778 (m-40) cc_final: 0.8358 (m-40) REVERT: B 479 GLN cc_start: 0.8285 (tp40) cc_final: 0.7491 (mp10) REVERT: B 594 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 605 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8304 (ttpp) REVERT: B 617 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7452 (ptm160) REVERT: B 637 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7612 (ptm-80) REVERT: B 656 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6932 (mtm-85) REVERT: B 677 ASP cc_start: 0.7594 (t70) cc_final: 0.7347 (t0) REVERT: B 690 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6478 (mtt90) REVERT: B 794 ASP cc_start: 0.7161 (t70) cc_final: 0.6701 (t0) REVERT: B 808 ASP cc_start: 0.8518 (m-30) cc_final: 0.8144 (m-30) REVERT: B 837 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7201 (tt0) outliers start: 39 outliers final: 20 residues processed: 213 average time/residue: 0.5627 time to fit residues: 130.9530 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 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 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN 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 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: 0.7980 chunk 164 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 156 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123121 restraints weight = 15169.198| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.79 r_work: 0.3123 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1703 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= 0.123 Angle : 0.509 6.460 20469 Z= 0.269 Chirality : 0.040 0.149 2298 Planarity : 0.005 0.060 2418 Dihedral : 14.445 85.398 2702 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.44 % Allowed : 15.83 % 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: 0.78 (0.21), residues: 1638 helix: 1.36 (0.20), residues: 658 sheet: -0.71 (0.32), residues: 238 loop : 0.34 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 689 TYR 0.024 0.001 TYR B 681 PHE 0.011 0.001 PHE A 620 TRP 0.009 0.001 TRP B 332 HIS 0.006 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14958) covalent geometry : angle 0.50734 / 0.27 (20463) hydrogen bonds : bond 0.04272 / 3.10 ( 645) hydrogen bonds : angle 4.50147 / 3.29 ( 1789) metal coordination : bond 0.01123 / 0.72 ( 8) metal coordination : angle 2.68222 / 5.73 ( 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 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 102 CYS cc_start: 0.8625 (t) cc_final: 0.8148 (m) REVERT: A 200 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: A 265 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8274 (m) REVERT: A 335 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: A 385 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8092 (mmtm) REVERT: A 414 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6913 (mtm110) REVERT: A 431 MET cc_start: 0.8833 (mmt) cc_final: 0.8347 (mmp) REVERT: A 482 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6146 (tm-30) REVERT: A 485 ASP cc_start: 0.8603 (t70) cc_final: 0.8305 (t0) REVERT: A 649 GLU cc_start: 0.7890 (mp0) cc_final: 0.7540 (mp0) REVERT: A 729 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7767 (mtt90) REVERT: A 830 MET cc_start: 0.7460 (tpp) cc_final: 0.6777 (mmm) REVERT: A 848 HIS cc_start: 0.8180 (m-70) cc_final: 0.7678 (m90) REVERT: B 11 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: B 38 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7840 (tp40) REVERT: B 301 ASN cc_start: 0.7946 (m-40) cc_final: 0.6914 (t0) REVERT: B 428 ASN cc_start: 0.8792 (m-40) cc_final: 0.8402 (m-40) REVERT: B 479 GLN cc_start: 0.8294 (tp40) cc_final: 0.7479 (mp10) REVERT: B 594 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: B 617 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7450 (ptm160) REVERT: B 637 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7686 (ptm-80) REVERT: B 656 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6886 (mtm-85) REVERT: B 677 ASP cc_start: 0.7594 (t70) cc_final: 0.7344 (t0) REVERT: B 690 ARG cc_start: 0.6661 (mtm110) cc_final: 0.6294 (mtt90) REVERT: B 794 ASP cc_start: 0.7249 (t70) cc_final: 0.6820 (t0) REVERT: B 808 ASP cc_start: 0.8519 (m-30) cc_final: 0.8175 (m-30) outliers start: 36 outliers final: 14 residues processed: 209 average time/residue: 0.6002 time to fit residues: 136.5919 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 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 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 637 ARG 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: 0.5980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.168449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123946 restraints weight = 15258.274| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.77 r_work: 0.3163 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1840 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= 0.125 Angle : 0.505 6.148 20469 Z= 0.266 Chirality : 0.040 0.148 2298 Planarity : 0.005 0.067 2418 Dihedral : 14.383 84.961 2702 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.03 % Allowed : 16.17 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.44 (0.20), residues: 660 sheet: -0.49 (0.33), residues: 236 loop : 0.34 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 689 TYR 0.023 0.001 TYR B 681 PHE 0.011 0.001 PHE B 435 TRP 0.008 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14958) covalent geometry : angle 0.50347 / 0.27 (20463) hydrogen bonds : bond 0.04165 / 3.03 ( 645) hydrogen bonds : angle 4.46500 / 3.26 ( 1789) metal coordination : bond 0.01045 / 0.68 ( 8) metal coordination : angle 2.51527 / 5.42 ( 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 226 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 102 CYS cc_start: 0.8620 (t) cc_final: 0.8170 (m) REVERT: A 200 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: A 265 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (m) REVERT: A 335 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: A 431 MET cc_start: 0.8856 (mmt) cc_final: 0.8395 (mmp) REVERT: A 482 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6117 (tm-30) REVERT: A 485 ASP cc_start: 0.8595 (t70) cc_final: 0.8299 (t0) REVERT: A 649 GLU cc_start: 0.7886 (mp0) cc_final: 0.7529 (mp0) REVERT: A 729 ARG cc_start: 0.8247 (mtt90) cc_final: 0.7783 (mtt90) REVERT: A 783 LEU cc_start: 0.7744 (mp) cc_final: 0.7539 (mp) REVERT: A 818 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 830 MET cc_start: 0.7436 (tpp) cc_final: 0.6759 (mmm) REVERT: A 848 HIS cc_start: 0.8173 (m-70) cc_final: 0.7528 (m-70) REVERT: B 11 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: B 38 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: B 428 ASN cc_start: 0.8779 (m-40) cc_final: 0.8426 (m-40) REVERT: B 479 GLN cc_start: 0.8304 (tp40) cc_final: 0.7487 (mp10) REVERT: B 617 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7465 (ptm160) REVERT: B 626 ARG cc_start: 0.7112 (mmp-170) cc_final: 0.6721 (mmp-170) REVERT: B 637 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7668 (ptm-80) REVERT: B 656 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6894 (mtm-85) REVERT: B 677 ASP cc_start: 0.7583 (t70) cc_final: 0.7335 (t0) REVERT: B 690 ARG cc_start: 0.6587 (mtm110) cc_final: 0.6280 (mtt90) REVERT: B 794 ASP cc_start: 0.7255 (t70) cc_final: 0.6800 (t0) REVERT: B 808 ASP cc_start: 0.8563 (m-30) cc_final: 0.8134 (m-30) outliers start: 30 outliers final: 13 residues processed: 215 average time/residue: 0.6319 time to fit residues: 147.9773 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 GLU 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 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 514 VAL Chi-restraints excluded: chain B residue 637 ARG 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: 3.9990 chunk 157 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.167828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122874 restraints weight = 15206.870| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.79 r_work: 0.3110 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14966 Z= 0.158 Angle : 0.526 6.601 20469 Z= 0.276 Chirality : 0.041 0.161 2298 Planarity : 0.005 0.095 2418 Dihedral : 14.383 84.758 2702 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.96 % Allowed : 16.85 % Favored : 81.19 % 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: 0.83 (0.21), residues: 1638 helix: 1.38 (0.20), residues: 660 sheet: -0.45 (0.32), residues: 244 loop : 0.30 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 414 TYR 0.021 0.001 TYR A 681 PHE 0.012 0.001 PHE A 620 TRP 0.010 0.001 TRP B 332 HIS 0.006 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (14958) covalent geometry : angle 0.52441 / 0.28 (20463) hydrogen bonds : bond 0.04257 / 3.10 ( 645) hydrogen bonds : angle 4.49780 / 3.29 ( 1789) metal coordination : bond 0.00928 / 0.61 ( 8) metal coordination : angle 2.56625 / 5.48 ( 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 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 102 CYS cc_start: 0.8621 (t) cc_final: 0.8170 (m) REVERT: A 200 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: A 262 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8257 (ttmm) REVERT: A 265 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 335 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: A 385 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8085 (mmtm) REVERT: A 414 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6896 (mtm110) REVERT: A 482 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6113 (tm-30) REVERT: A 485 ASP cc_start: 0.8612 (t70) cc_final: 0.8306 (t0) REVERT: A 649 GLU cc_start: 0.7896 (mp0) cc_final: 0.7530 (mp0) REVERT: A 729 ARG cc_start: 0.8251 (mtt90) cc_final: 0.7787 (mtt90) REVERT: A 818 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: A 830 MET cc_start: 0.7430 (tpp) cc_final: 0.6615 (mmm) REVERT: A 848 HIS cc_start: 0.8187 (m-70) cc_final: 0.7527 (m-70) REVERT: B 11 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: B 38 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7847 (tp40) REVERT: B 301 ASN cc_start: 0.7939 (m-40) cc_final: 0.6945 (t0) REVERT: B 428 ASN cc_start: 0.8783 (m-40) cc_final: 0.8429 (m-40) REVERT: B 479 GLN cc_start: 0.8314 (tp40) cc_final: 0.7467 (mp10) REVERT: B 617 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7451 (ptm160) REVERT: B 626 ARG cc_start: 0.7036 (mmp-170) cc_final: 0.6673 (mmp-170) REVERT: B 637 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7617 (ptm-80) REVERT: B 656 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6884 (mtm-85) REVERT: B 677 ASP cc_start: 0.7588 (t70) cc_final: 0.7333 (t0) REVERT: B 690 ARG cc_start: 0.6698 (mtm110) cc_final: 0.6413 (mtt90) REVERT: B 794 ASP cc_start: 0.7257 (t70) cc_final: 0.6827 (t0) REVERT: B 808 ASP cc_start: 0.8547 (m-30) cc_final: 0.8141 (m-30) outliers start: 29 outliers final: 16 residues processed: 207 average time/residue: 0.5995 time to fit residues: 135.1849 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 748 ILE 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 145 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 0.0970 chunk 106 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124622 restraints weight = 15032.330| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.79 r_work: 0.3133 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14966 Z= 0.116 Angle : 0.507 7.345 20469 Z= 0.266 Chirality : 0.039 0.150 2298 Planarity : 0.005 0.083 2418 Dihedral : 14.353 84.279 2702 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.49 % Allowed : 17.32 % Favored : 81.19 % 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: 0.98 (0.21), residues: 1638 helix: 1.50 (0.20), residues: 660 sheet: -0.37 (0.33), residues: 232 loop : 0.36 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 414 TYR 0.021 0.001 TYR B 681 PHE 0.015 0.001 PHE A 620 TRP 0.007 0.001 TRP B 413 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14958) covalent geometry : angle 0.50528 / 0.27 (20463) hydrogen bonds : bond 0.04072 / 2.96 ( 645) hydrogen bonds : angle 4.44548 / 3.24 ( 1789) metal coordination : bond 0.01127 / 0.72 ( 8) metal coordination : angle 2.56796 / 5.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4907.47 seconds wall clock time: 84 minutes 17.53 seconds (5057.53 seconds total)