Starting phenix.real_space_refine on Thu Sep 18 05:50:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_19913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_19913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_19913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_19913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_19913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ere_19913/09_2025/9ere_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14541 Number of models: 1 Model: "" Number of chains: 7 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "T" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1119 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 9, 'rna3p': 42} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2116 SG CYS A 287 73.993 60.501 71.377 1.00 55.34 S ATOM 2393 SG CYS A 321 73.713 59.016 67.866 1.00 50.25 S ATOM 2399 SG CYS A 322 71.160 61.546 69.077 1.00 53.20 S ATOM 8781 SG CYS B 287 22.980 71.162 71.471 1.00 62.19 S ATOM 9058 SG CYS B 321 22.983 72.191 67.850 1.00 47.88 S ATOM 9064 SG CYS B 322 25.569 69.827 69.210 1.00 48.25 S Time building chain proxies: 3.73, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 594.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.99 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: 3.15 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2226 1.28 - 1.41: 3908 1.41 - 1.55: 8591 1.55 - 1.68: 111 1.68 - 1.81: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ARG B 729 " pdb=" C ARG B 729 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.24e-02 6.50e+03 7.03e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.234 1.148 0.087 1.26e-02 6.30e+03 4.72e+01 bond pdb=" C ARG A 862 " pdb=" O ARG A 862 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.22e-02 6.72e+03 3.04e+01 bond pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.82e+01 bond pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.21e-02 6.83e+03 2.35e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19984 1.78 - 3.56: 398 3.56 - 5.35: 68 5.35 - 7.13: 10 7.13 - 8.91: 3 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.71 120.44 -8.73 1.15e+00 7.56e-01 5.77e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 111.28 117.35 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" C GLN A 774 " ideal model delta sigma weight residual 110.20 118.26 -8.06 1.58e+00 4.01e-01 2.60e+01 angle pdb=" C PRO A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.84 113.57 6.27 1.25e+00 6.40e-01 2.51e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8229 19.09 - 38.18: 626 38.18 - 57.26: 221 57.26 - 76.35: 105 76.35 - 95.44: 18 Dihedral angle restraints: 9199 sinusoidal: 4367 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 136.56 95.44 1 1.70e+01 3.46e-03 3.64e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C ARG B 729 " pdb=" N ARG B 729 " pdb=" CA ARG B 729 " pdb=" CB ARG B 729 " ideal model delta harmonic sigma weight residual -122.60 -112.06 -10.54 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2067 0.067 - 0.134: 221 0.134 - 0.202: 6 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA LEU B 636 " pdb=" N LEU B 636 " pdb=" C LEU B 636 " pdb=" CB LEU B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN A 706 " pdb=" N GLN A 706 " pdb=" C GLN A 706 " pdb=" CB GLN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 705 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 705 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE A 705 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 706 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 851 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LEU A 851 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 851 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 852 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C THR B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O THR B 728 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 729 " -0.018 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 10482 3.10 - 3.70: 23246 3.70 - 4.30: 35303 4.30 - 4.90: 57539 Nonbonded interactions: 126660 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 1.903 2.320 nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.918 2.170 nonbonded pdb=" OD2 ASP A 252 " pdb="MN MN A1002 " model vdw 1.927 2.320 nonbonded pdb=" OE2 GLU A 209 " pdb="MN MN A1002 " model vdw 2.051 2.320 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 2.062 2.320 ... (remaining 126655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 7 through 1002) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 14966 Z= 0.265 Angle : 0.644 8.911 20469 Z= 0.369 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 aren 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 covalent geometry : bond 0.00488 (14958) covalent geometry : angle 0.64059 (20463) hydrogen bonds : bond 0.12258 ( 645) hydrogen bonds : angle 5.74508 ( 1789) metal coordination : bond 0.01942 ( 8) metal coordination : angle 3.71606 ( 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 : 0.602 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: 0.8309 time to fit residues: 193.0571 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 : 0.534 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 625 HIS B 195 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 = 0.3851 r_free = 0.3851 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121229 restraints weight = 15158.641| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.85 r_work: 0.3079 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14966 Z= 0.180 Angle : 0.572 8.497 20469 Z= 0.297 Chirality : 0.042 0.155 2298 Planarity : 0.005 0.051 2418 Dihedral : 14.755 96.853 2710 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.64 % Allowed : 11.98 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1638 helix: 1.17 (0.20), residues: 658 sheet: -0.56 (0.30), residues: 244 loop : 0.39 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.018 0.002 TYR A 234 PHE 0.014 0.002 PHE A 435 TRP 0.012 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00426 (14958) covalent geometry : angle 0.56923 (20463) hydrogen bonds : bond 0.04733 ( 645) hydrogen bonds : angle 4.78862 ( 1789) metal coordination : bond 0.01432 ( 8) metal coordination : angle 3.61128 ( 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 239 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: A 200 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: A 219 SER cc_start: 0.8911 (t) cc_final: 0.8645 (p) REVERT: A 290 GLN cc_start: 0.8223 (mt0) cc_final: 0.7977 (mp10) REVERT: A 385 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8085 (mmtm) REVERT: A 453 GLU cc_start: 0.8046 (tt0) cc_final: 0.7686 (tp30) REVERT: A 482 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6322 (tm-30) REVERT: A 649 GLU cc_start: 0.8044 (mp0) cc_final: 0.7525 (mp0) REVERT: A 729 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7949 (mtt90) REVERT: A 818 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6564 (mp0) REVERT: A 848 HIS cc_start: 0.8146 (m-70) cc_final: 0.7633 (m90) REVERT: B 11 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: B 38 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: B 198 TYR cc_start: 0.7806 (p90) cc_final: 0.7558 (p90) REVERT: B 262 LYS cc_start: 0.7811 (ptmt) cc_final: 0.7515 (ptpt) REVERT: B 428 ASN cc_start: 0.8606 (m-40) cc_final: 0.8207 (m-40) REVERT: B 479 GLN cc_start: 0.8334 (tp40) cc_final: 0.7552 (mp10) REVERT: B 594 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: B 608 MET cc_start: 0.8738 (mmt) cc_final: 0.8524 (mmt) REVERT: B 617 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7627 (ptm160) REVERT: B 677 ASP cc_start: 0.7687 (t0) cc_final: 0.7484 (t0) REVERT: B 794 ASP cc_start: 0.7255 (t70) cc_final: 0.6822 (t0) outliers start: 39 outliers final: 11 residues processed: 226 average time/residue: 0.7667 time to fit residues: 187.5312 Evaluate side-chains 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 776 THR 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: 0.0980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 638 ASN B 224 GLN B 663 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 = 0.3854 r_free = 0.3854 target = 0.166804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121357 restraints weight = 15295.778| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.86 r_work: 0.3080 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14966 Z= 0.164 Angle : 0.545 8.582 20469 Z= 0.280 Chirality : 0.041 0.154 2298 Planarity : 0.005 0.047 2418 Dihedral : 14.569 93.656 2705 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.98 % Allowed : 12.31 % Favored : 84.71 % 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 aren not related in a simple way. whole: 0.71 (0.21), residues: 1638 helix: 1.21 (0.20), residues: 656 sheet: -0.65 (0.31), residues: 244 loop : 0.37 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 414 TYR 0.020 0.001 TYR B 681 PHE 0.011 0.001 PHE A 435 TRP 0.011 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00386 (14958) covalent geometry : angle 0.54205 (20463) hydrogen bonds : bond 0.04431 ( 645) hydrogen bonds : angle 4.62535 ( 1789) metal coordination : bond 0.01159 ( 8) metal coordination : angle 3.29275 ( 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 237 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 200 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: A 219 SER cc_start: 0.8916 (t) cc_final: 0.8707 (p) REVERT: A 335 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: A 385 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8102 (mmtm) REVERT: A 453 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 482 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6307 (tm-30) REVERT: A 485 ASP cc_start: 0.8655 (t70) cc_final: 0.8342 (t0) REVERT: A 649 GLU cc_start: 0.7932 (mp0) cc_final: 0.7526 (mp0) REVERT: A 729 ARG cc_start: 0.8250 (mtt90) cc_final: 0.8030 (mtt90) REVERT: A 830 MET cc_start: 0.7480 (tpp) cc_final: 0.6910 (mmm) REVERT: A 848 HIS cc_start: 0.8139 (m-70) cc_final: 0.7666 (m90) REVERT: B 11 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: B 38 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7852 (tp40) REVERT: B 195 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8147 (mm-40) REVERT: B 198 TYR cc_start: 0.7794 (p90) cc_final: 0.7538 (p90) REVERT: B 233 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: B 428 ASN cc_start: 0.8753 (m-40) cc_final: 0.8329 (m-40) REVERT: B 479 GLN cc_start: 0.8358 (tp40) cc_final: 0.7514 (mp10) REVERT: B 594 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 608 MET cc_start: 0.8730 (mmt) cc_final: 0.8507 (mmt) REVERT: B 617 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7562 (ptm160) REVERT: B 637 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7635 (ptm-80) REVERT: B 677 ASP cc_start: 0.7837 (t0) cc_final: 0.7591 (t0) REVERT: B 794 ASP cc_start: 0.7323 (t70) cc_final: 0.6885 (t0) REVERT: B 808 ASP cc_start: 0.8644 (m-30) cc_final: 0.8306 (m-30) outliers start: 44 outliers final: 15 residues processed: 218 average time/residue: 0.8082 time to fit residues: 190.4878 Evaluate side-chains 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 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 195 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS B 195 GLN B 224 GLN B 276 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119924 restraints weight = 15261.258| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.88 r_work: 0.3056 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1361 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= 0.219 Angle : 0.574 8.391 20469 Z= 0.293 Chirality : 0.042 0.152 2298 Planarity : 0.005 0.053 2418 Dihedral : 14.525 91.085 2702 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.32 % Allowed : 13.26 % Favored : 83.42 % 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 aren not related in a simple way. whole: 0.58 (0.21), residues: 1638 helix: 1.10 (0.20), residues: 658 sheet: -0.69 (0.31), residues: 244 loop : 0.29 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 414 TYR 0.025 0.002 TYR B 681 PHE 0.013 0.002 PHE A 620 TRP 0.014 0.002 TRP B 332 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00523 (14958) covalent geometry : angle 0.57142 (20463) hydrogen bonds : bond 0.04585 ( 645) hydrogen bonds : angle 4.64330 ( 1789) metal coordination : bond 0.01036 ( 8) metal coordination : angle 2.96590 ( 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 238 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: A 200 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: A 335 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: A 337 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8708 (ptmm) REVERT: A 453 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: A 482 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6304 (tm-30) REVERT: A 697 ILE cc_start: 0.8923 (mm) cc_final: 0.8718 (mt) REVERT: A 729 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7995 (mtt90) REVERT: A 830 MET cc_start: 0.7471 (tpp) cc_final: 0.6810 (mmm) REVERT: A 848 HIS cc_start: 0.8225 (m-70) cc_final: 0.7623 (m-70) REVERT: B 11 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: B 38 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (tp40) REVERT: B 195 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: B 198 TYR cc_start: 0.7886 (p90) cc_final: 0.7576 (p90) REVERT: B 233 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: B 262 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7545 (ptpt) REVERT: B 428 ASN cc_start: 0.8786 (m-40) cc_final: 0.8312 (m-40) REVERT: B 479 GLN cc_start: 0.8319 (tp40) cc_final: 0.7502 (mp10) REVERT: B 594 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 617 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7532 (ptm160) REVERT: B 677 ASP cc_start: 0.7782 (t0) cc_final: 0.7520 (t0) REVERT: B 794 ASP cc_start: 0.7281 (t70) cc_final: 0.6840 (t0) outliers start: 49 outliers final: 18 residues processed: 218 average time/residue: 0.8079 time to fit residues: 190.6290 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain 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 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.167149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121835 restraints weight = 15196.229| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.82 r_work: 0.3122 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14966 Z= 0.135 Angle : 0.521 8.367 20469 Z= 0.267 Chirality : 0.040 0.150 2298 Planarity : 0.004 0.057 2418 Dihedral : 14.440 88.642 2702 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.64 % Allowed : 14.61 % Favored : 82.75 % 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 aren not related in a simple way. whole: 0.71 (0.21), residues: 1638 helix: 1.26 (0.20), residues: 658 sheet: -0.68 (0.31), residues: 244 loop : 0.32 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 414 TYR 0.015 0.001 TYR A 234 PHE 0.009 0.001 PHE B 151 TRP 0.010 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00313 (14958) covalent geometry : angle 0.51885 (20463) hydrogen bonds : bond 0.04140 ( 645) hydrogen bonds : angle 4.50890 ( 1789) metal coordination : bond 0.01145 ( 8) metal coordination : angle 2.84000 ( 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: 39 poor density : 194 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: A 200 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: A 265 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7715 (m) REVERT: A 335 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: A 385 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8124 (mmtm) REVERT: A 414 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6821 (mtm110) REVERT: A 431 MET cc_start: 0.8874 (mmt) cc_final: 0.8378 (mmp) REVERT: A 482 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6227 (tm-30) REVERT: A 485 ASP cc_start: 0.8733 (t70) cc_final: 0.8471 (t0) REVERT: A 649 GLU cc_start: 0.7947 (mp0) cc_final: 0.7507 (mp0) REVERT: A 729 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7749 (mtt90) REVERT: A 830 MET cc_start: 0.7462 (tpp) cc_final: 0.6727 (mmm) REVERT: A 848 HIS cc_start: 0.8189 (m-70) cc_final: 0.7716 (m90) REVERT: B 11 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: B 195 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (mm-40) REVERT: B 198 TYR cc_start: 0.7856 (p90) cc_final: 0.7587 (p90) REVERT: B 262 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7565 (ptpt) REVERT: B 428 ASN cc_start: 0.8805 (m-40) cc_final: 0.8407 (m-40) REVERT: B 479 GLN cc_start: 0.8294 (tp40) cc_final: 0.7476 (mp10) REVERT: B 605 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8272 (ttpp) REVERT: B 617 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7485 (ptm160) REVERT: B 637 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7630 (ptm-80) REVERT: B 677 ASP cc_start: 0.7687 (t0) cc_final: 0.7404 (t0) REVERT: B 794 ASP cc_start: 0.7196 (t70) cc_final: 0.6746 (t0) REVERT: B 808 ASP cc_start: 0.8586 (m-30) cc_final: 0.8207 (m-30) outliers start: 39 outliers final: 14 residues processed: 219 average time/residue: 0.7846 time to fit residues: 186.4587 Evaluate side-chains 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 95 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121492 restraints weight = 15237.882| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.90 r_work: 0.3109 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14966 Z= 0.118 Angle : 0.502 8.184 20469 Z= 0.258 Chirality : 0.040 0.172 2298 Planarity : 0.004 0.041 2418 Dihedral : 14.341 85.734 2702 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.77 % Allowed : 15.09 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 660 sheet: -0.58 (0.32), residues: 244 loop : 0.33 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 689 TYR 0.018 0.001 TYR B 681 PHE 0.010 0.001 PHE A 620 TRP 0.008 0.001 TRP B 332 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00271 (14958) covalent geometry : angle 0.50007 (20463) hydrogen bonds : bond 0.03957 ( 645) hydrogen bonds : angle 4.40867 ( 1789) metal coordination : bond 0.01132 ( 8) metal coordination : angle 2.60457 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 200 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: A 265 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 335 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: A 431 MET cc_start: 0.8800 (mmt) cc_final: 0.8332 (mmp) REVERT: A 482 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6256 (tm-30) REVERT: A 485 ASP cc_start: 0.8750 (t70) cc_final: 0.8482 (t0) REVERT: A 649 GLU cc_start: 0.7922 (mp0) cc_final: 0.7475 (mp0) REVERT: A 729 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7799 (mtt90) REVERT: A 830 MET cc_start: 0.7377 (tpp) cc_final: 0.6649 (mmm) REVERT: A 848 HIS cc_start: 0.8206 (m-70) cc_final: 0.7582 (m-70) REVERT: B 11 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 195 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8121 (mm-40) REVERT: B 198 TYR cc_start: 0.7780 (p90) cc_final: 0.7458 (p90) REVERT: B 273 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (tttp) REVERT: B 428 ASN cc_start: 0.8777 (m-40) cc_final: 0.8442 (m-40) REVERT: B 479 GLN cc_start: 0.8288 (tp40) cc_final: 0.7460 (mp10) REVERT: B 594 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: B 617 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7427 (ptm160) REVERT: B 637 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (ptm-80) REVERT: B 656 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6902 (mtm-85) REVERT: B 677 ASP cc_start: 0.7618 (t0) cc_final: 0.7367 (t0) REVERT: B 690 ARG cc_start: 0.6634 (mtm110) cc_final: 0.6322 (mtt90) REVERT: B 794 ASP cc_start: 0.7239 (t70) cc_final: 0.6793 (t0) REVERT: B 808 ASP cc_start: 0.8567 (m-30) cc_final: 0.8174 (m-30) REVERT: B 884 CYS cc_start: 0.8045 (t) cc_final: 0.7456 (m) outliers start: 41 outliers final: 14 residues processed: 220 average time/residue: 0.7785 time to fit residues: 185.6079 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 276 GLN B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120287 restraints weight = 15118.498| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.89 r_work: 0.3074 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1749 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= 0.179 Angle : 0.542 8.002 20469 Z= 0.277 Chirality : 0.041 0.148 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.352 84.684 2702 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.77 % Allowed : 15.09 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1638 helix: 1.35 (0.20), residues: 658 sheet: -0.61 (0.32), residues: 244 loop : 0.27 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 414 TYR 0.025 0.002 TYR B 681 PHE 0.011 0.001 PHE B 151 TRP 0.011 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00427 (14958) covalent geometry : angle 0.54000 (20463) hydrogen bonds : bond 0.04240 ( 645) hydrogen bonds : angle 4.49048 ( 1789) metal coordination : bond 0.00820 ( 8) metal coordination : angle 2.56747 ( 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 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: A 102 CYS cc_start: 0.8575 (t) cc_final: 0.8175 (m) REVERT: A 200 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: A 265 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7779 (m) REVERT: A 335 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: A 351 MET cc_start: 0.8919 (mmm) cc_final: 0.8491 (mmm) REVERT: A 385 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8103 (mmtm) REVERT: A 414 ARG cc_start: 0.7185 (mtm110) cc_final: 0.6757 (mtm110) REVERT: A 482 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6152 (tm-30) REVERT: A 485 ASP cc_start: 0.8786 (t70) cc_final: 0.8501 (t0) REVERT: A 649 GLU cc_start: 0.7947 (mp0) cc_final: 0.7586 (mp0) REVERT: A 729 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7821 (mtt90) REVERT: A 830 MET cc_start: 0.7408 (tpp) cc_final: 0.6955 (mmm) REVERT: A 848 HIS cc_start: 0.8235 (m-70) cc_final: 0.7607 (m-70) REVERT: B 11 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: B 195 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (mm-40) REVERT: B 198 TYR cc_start: 0.7833 (p90) cc_final: 0.7523 (p90) REVERT: B 301 ASN cc_start: 0.7971 (m-40) cc_final: 0.6938 (t0) REVERT: B 428 ASN cc_start: 0.8848 (m-40) cc_final: 0.8478 (m-40) REVERT: B 479 GLN cc_start: 0.8315 (tp40) cc_final: 0.7427 (mp10) REVERT: B 594 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: B 617 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7398 (ptm160) REVERT: B 647 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8181 (ttp-170) REVERT: B 677 ASP cc_start: 0.7623 (t0) cc_final: 0.7368 (t0) REVERT: B 690 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6468 (mtt90) REVERT: B 794 ASP cc_start: 0.7223 (t70) cc_final: 0.6769 (t0) REVERT: B 808 ASP cc_start: 0.8587 (m-30) cc_final: 0.8222 (m-30) outliers start: 41 outliers final: 23 residues processed: 218 average time/residue: 0.7565 time to fit residues: 178.3419 Evaluate side-chains 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 497 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 224 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.168375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122545 restraints weight = 15242.032| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.88 r_work: 0.3128 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14966 Z= 0.123 Angle : 0.511 7.896 20469 Z= 0.262 Chirality : 0.039 0.150 2298 Planarity : 0.004 0.059 2418 Dihedral : 14.292 83.289 2702 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 15.22 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.21), residues: 1638 helix: 1.49 (0.20), residues: 660 sheet: -0.53 (0.32), residues: 244 loop : 0.31 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 414 TYR 0.023 0.001 TYR B 681 PHE 0.010 0.001 PHE B 435 TRP 0.008 0.001 TRP B 332 HIS 0.007 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00285 (14958) covalent geometry : angle 0.50919 (20463) hydrogen bonds : bond 0.03959 ( 645) hydrogen bonds : angle 4.40918 ( 1789) metal coordination : bond 0.01089 ( 8) metal coordination : angle 2.45593 ( 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 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: A 102 CYS cc_start: 0.8606 (t) cc_final: 0.8167 (m) REVERT: A 200 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: A 265 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7726 (m) REVERT: A 335 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: A 414 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6917 (mtm110) REVERT: A 482 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6194 (tm-30) REVERT: A 485 ASP cc_start: 0.8746 (t70) cc_final: 0.8476 (t0) REVERT: A 533 MET cc_start: 0.8071 (ttm) cc_final: 0.7778 (tpp) REVERT: A 649 GLU cc_start: 0.7926 (mp0) cc_final: 0.7577 (mp0) REVERT: A 674 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6590 (mtt-85) REVERT: A 729 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7818 (mtt90) REVERT: A 830 MET cc_start: 0.7427 (tpp) cc_final: 0.7027 (mmm) REVERT: A 848 HIS cc_start: 0.8195 (m-70) cc_final: 0.7721 (m90) REVERT: B 11 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: B 195 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8096 (mm-40) REVERT: B 198 TYR cc_start: 0.7794 (p90) cc_final: 0.7527 (p90) REVERT: B 229 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7125 (ptp-110) REVERT: B 301 ASN cc_start: 0.7950 (m-40) cc_final: 0.7006 (t0) REVERT: B 428 ASN cc_start: 0.8797 (m-40) cc_final: 0.8441 (m-40) REVERT: B 479 GLN cc_start: 0.8335 (tp40) cc_final: 0.7437 (mp10) REVERT: B 594 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: B 617 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7399 (ptm160) REVERT: B 637 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7617 (ptm-80) REVERT: B 677 ASP cc_start: 0.7645 (t70) cc_final: 0.7397 (t0) REVERT: B 794 ASP cc_start: 0.7212 (t70) cc_final: 0.6761 (t0) REVERT: B 808 ASP cc_start: 0.8554 (m-30) cc_final: 0.8230 (m-30) outliers start: 40 outliers final: 18 residues processed: 217 average time/residue: 0.8032 time to fit residues: 188.7602 Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 241 THR 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 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 788 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121795 restraints weight = 15265.224| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.89 r_work: 0.3099 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14966 Z= 0.147 Angle : 0.530 7.703 20469 Z= 0.270 Chirality : 0.040 0.149 2298 Planarity : 0.005 0.060 2418 Dihedral : 14.281 82.761 2702 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 15.49 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1638 helix: 1.47 (0.20), residues: 660 sheet: -0.51 (0.32), residues: 244 loop : 0.29 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 689 TYR 0.026 0.001 TYR B 681 PHE 0.010 0.001 PHE B 435 TRP 0.009 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00348 (14958) covalent geometry : angle 0.52833 (20463) hydrogen bonds : bond 0.04055 ( 645) hydrogen bonds : angle 4.43450 ( 1789) metal coordination : bond 0.00923 ( 8) metal coordination : angle 2.45900 ( 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: 38 poor density : 188 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: A 102 CYS cc_start: 0.8602 (t) cc_final: 0.8179 (m) REVERT: A 200 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: A 265 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7865 (m) REVERT: A 335 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 414 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6802 (mtm110) REVERT: A 452 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 482 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6153 (tm-30) REVERT: A 485 ASP cc_start: 0.8708 (t70) cc_final: 0.8408 (t0) REVERT: A 533 MET cc_start: 0.8031 (ttm) cc_final: 0.7742 (tpp) REVERT: A 617 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7650 (ttp-170) REVERT: A 649 GLU cc_start: 0.7935 (mp0) cc_final: 0.7580 (mp0) REVERT: A 729 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7804 (mtt90) REVERT: A 830 MET cc_start: 0.7424 (tpp) cc_final: 0.7022 (mmm) REVERT: A 848 HIS cc_start: 0.8242 (m-70) cc_final: 0.7612 (m-70) REVERT: B 11 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: B 195 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (mm-40) REVERT: B 198 TYR cc_start: 0.7776 (p90) cc_final: 0.7523 (p90) REVERT: B 229 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7145 (ptp-110) REVERT: B 273 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8229 (tttp) REVERT: B 301 ASN cc_start: 0.7942 (m-40) cc_final: 0.6947 (t0) REVERT: B 428 ASN cc_start: 0.8797 (m-40) cc_final: 0.8417 (m110) REVERT: B 479 GLN cc_start: 0.8342 (tp40) cc_final: 0.7422 (mp10) REVERT: B 594 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 617 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7370 (ptm160) REVERT: B 626 ARG cc_start: 0.6984 (mmp-170) cc_final: 0.6767 (mmp-170) REVERT: B 677 ASP cc_start: 0.7645 (t70) cc_final: 0.7382 (t0) REVERT: B 690 ARG cc_start: 0.6480 (mtm110) cc_final: 0.6166 (mtt90) REVERT: B 789 MET cc_start: 0.7444 (tpp) cc_final: 0.6971 (tpt) REVERT: B 794 ASP cc_start: 0.7327 (t70) cc_final: 0.6889 (t0) REVERT: B 808 ASP cc_start: 0.8565 (m-30) cc_final: 0.8129 (m-30) outliers start: 38 outliers final: 17 residues processed: 211 average time/residue: 0.7964 time to fit residues: 181.5979 Evaluate side-chains 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 157 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 0.2980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.169123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123424 restraints weight = 15261.746| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3130 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14966 Z= 0.123 Angle : 0.515 7.426 20469 Z= 0.263 Chirality : 0.039 0.151 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.240 82.031 2702 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.96 % Allowed : 16.31 % 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 aren not related in a simple way. whole: 0.96 (0.21), residues: 1638 helix: 1.58 (0.20), residues: 660 sheet: -0.50 (0.32), residues: 246 loop : 0.32 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 689 TYR 0.024 0.001 TYR B 681 PHE 0.011 0.001 PHE B 435 TRP 0.008 0.001 TRP B 332 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00287 (14958) covalent geometry : angle 0.51306 (20463) hydrogen bonds : bond 0.03916 ( 645) hydrogen bonds : angle 4.40183 ( 1789) metal coordination : bond 0.01088 ( 8) metal coordination : angle 2.30198 ( 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 226 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: A 102 CYS cc_start: 0.8590 (t) cc_final: 0.8168 (m) REVERT: A 265 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7884 (m) REVERT: A 335 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: A 336 ASP cc_start: 0.7393 (m-30) cc_final: 0.6969 (t70) REVERT: A 384 LYS cc_start: 0.7338 (mppt) cc_final: 0.7090 (mptm) REVERT: A 414 ARG cc_start: 0.7178 (mtm110) cc_final: 0.6952 (mtm110) REVERT: A 482 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6218 (tm-30) REVERT: A 485 ASP cc_start: 0.8644 (t70) cc_final: 0.8354 (t0) REVERT: A 533 MET cc_start: 0.8026 (ttm) cc_final: 0.7733 (tpp) REVERT: A 649 GLU cc_start: 0.7928 (mp0) cc_final: 0.7577 (mp0) REVERT: A 729 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7831 (mtt90) REVERT: A 830 MET cc_start: 0.7457 (tpp) cc_final: 0.7101 (mmm) REVERT: A 848 HIS cc_start: 0.8225 (m-70) cc_final: 0.7605 (m-70) REVERT: B 11 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: B 195 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: B 198 TYR cc_start: 0.7742 (p90) cc_final: 0.7474 (p90) REVERT: B 229 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7133 (ptp-110) REVERT: B 272 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8373 (ttm-80) REVERT: B 301 ASN cc_start: 0.7933 (m-40) cc_final: 0.7053 (t0) REVERT: B 335 GLU cc_start: 0.7774 (pt0) cc_final: 0.7440 (pt0) REVERT: B 428 ASN cc_start: 0.8779 (m-40) cc_final: 0.8459 (m110) REVERT: B 479 GLN cc_start: 0.8328 (tp40) cc_final: 0.7371 (mp10) REVERT: B 594 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: B 617 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7369 (ptm160) REVERT: B 656 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.6508 (ptp90) REVERT: B 677 ASP cc_start: 0.7640 (t70) cc_final: 0.7375 (t0) REVERT: B 690 ARG cc_start: 0.6534 (mtm110) cc_final: 0.6214 (mtt90) REVERT: B 794 ASP cc_start: 0.7319 (t70) cc_final: 0.6902 (t0) REVERT: B 808 ASP cc_start: 0.8529 (m-30) cc_final: 0.8130 (m-30) outliers start: 29 outliers final: 17 residues processed: 216 average time/residue: 0.7637 time to fit residues: 178.5950 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 276 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 = 0.3888 r_free = 0.3888 target = 0.169595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123780 restraints weight = 15112.525| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.88 r_work: 0.3168 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14966 Z= 0.115 Angle : 0.513 7.481 20469 Z= 0.260 Chirality : 0.039 0.152 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.209 81.238 2702 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 16.64 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.21), residues: 1638 helix: 1.65 (0.21), residues: 660 sheet: -0.46 (0.33), residues: 246 loop : 0.31 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 689 TYR 0.022 0.001 TYR B 681 PHE 0.011 0.001 PHE B 435 TRP 0.008 0.001 TRP B 413 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00266 (14958) covalent geometry : angle 0.51116 (20463) hydrogen bonds : bond 0.03848 ( 645) hydrogen bonds : angle 4.37092 ( 1789) metal coordination : bond 0.00964 ( 8) metal coordination : angle 2.25830 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6445.61 seconds wall clock time: 110 minutes 34.16 seconds (6634.16 seconds total)