Starting phenix.real_space_refine on Tue Dec 31 01:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.map" model { file = "/net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ere_19913/12_2024/9ere_19913.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 56 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 9043 2.51 5 N 2541 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14541 Number of models: 1 Model: "" Number of chains: 7 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "T" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1119 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 9, 'rna3p': 42} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2116 SG CYS A 287 73.993 60.501 71.377 1.00 55.34 S ATOM 2393 SG CYS A 321 73.713 59.016 67.866 1.00 50.25 S ATOM 2399 SG CYS A 322 71.160 61.546 69.077 1.00 53.20 S ATOM 8781 SG CYS B 287 22.980 71.162 71.471 1.00 62.19 S ATOM 9058 SG CYS B 321 22.983 72.191 67.850 1.00 47.88 S ATOM 9064 SG CYS B 322 25.569 69.827 69.210 1.00 48.25 S Time building chain proxies: 9.15, per 1000 atoms: 0.63 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 18 sheets defined 44.6% alpha, 19.2% beta 23 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.186A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.540A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 398 removed outlier: 5.547A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 481 through 501 removed outlier: 4.513A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 563 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.589A pdb=" N ASN A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 757 through 763 removed outlier: 4.309A pdb=" N LEU A 761 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.648A pdb=" N ALA A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.579A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.284A pdb=" N PHE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 222 through 241 removed outlier: 4.085A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.655A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 398 removed outlier: 5.668A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 480 through 501 removed outlier: 4.484A pdb=" N GLN B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.626A pdb=" N ARG B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.638A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.507A pdb=" N GLN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 763 removed outlier: 3.771A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 762 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 Processing helix chain 'B' and resid 878 through 887 removed outlier: 4.309A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.663A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.425A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.425A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.512A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.166A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 595 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 702 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 597 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.105A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 810 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE A 868 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 812 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 11 removed outlier: 4.616A pdb=" N VAL B 18 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.796A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.796A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.497A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.486A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.062A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 810 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 868 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 812 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2226 1.28 - 1.41: 3908 1.41 - 1.55: 8591 1.55 - 1.68: 111 1.68 - 1.81: 122 Bond restraints: 14958 Sorted by residual: bond pdb=" CA ARG B 729 " pdb=" C ARG B 729 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.24e-02 6.50e+03 7.03e+01 bond pdb=" C ARG A 134 " pdb=" O ARG A 134 " ideal model delta sigma weight residual 1.234 1.148 0.087 1.26e-02 6.30e+03 4.72e+01 bond pdb=" C ARG A 862 " pdb=" O ARG A 862 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.22e-02 6.72e+03 3.04e+01 bond pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.82e+01 bond pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.21e-02 6.83e+03 2.35e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19984 1.78 - 3.56: 398 3.56 - 5.35: 68 5.35 - 7.13: 10 7.13 - 8.91: 3 Bond angle restraints: 20463 Sorted by residual: angle pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" C LEU B 636 " ideal model delta sigma weight residual 111.71 120.44 -8.73 1.15e+00 7.56e-01 5.77e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 111.28 117.35 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N ASN B 638 " pdb=" CA ASN B 638 " pdb=" C ASN B 638 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" C GLN A 774 " ideal model delta sigma weight residual 110.20 118.26 -8.06 1.58e+00 4.01e-01 2.60e+01 angle pdb=" C PRO A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.84 113.57 6.27 1.25e+00 6.40e-01 2.51e+01 ... (remaining 20458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8229 19.09 - 38.18: 626 38.18 - 57.26: 221 57.26 - 76.35: 105 76.35 - 95.44: 18 Dihedral angle restraints: 9199 sinusoidal: 4367 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 136.56 95.44 1 1.70e+01 3.46e-03 3.64e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C ARG B 729 " pdb=" N ARG B 729 " pdb=" CA ARG B 729 " pdb=" CB ARG B 729 " ideal model delta harmonic sigma weight residual -122.60 -112.06 -10.54 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2067 0.067 - 0.134: 221 0.134 - 0.202: 6 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA LEU B 636 " pdb=" N LEU B 636 " pdb=" C LEU B 636 " pdb=" CB LEU B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN A 706 " pdb=" N GLN A 706 " pdb=" C GLN A 706 " pdb=" CB GLN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 705 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 705 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE A 705 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 706 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 851 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LEU A 851 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 851 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 852 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C THR B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O THR B 728 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 729 " -0.018 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 10482 3.10 - 3.70: 23246 3.70 - 4.30: 35303 4.30 - 4.90: 57539 Nonbonded interactions: 126660 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 1.903 2.320 nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.918 2.170 nonbonded pdb=" OD2 ASP A 252 " pdb="MN MN A1002 " model vdw 1.927 2.320 nonbonded pdb=" OE2 GLU A 209 " pdb="MN MN A1002 " model vdw 2.051 2.320 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 2.062 2.320 ... (remaining 126655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 7 through 899 or resid 1001 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 14958 Z= 0.314 Angle : 0.641 8.911 20463 Z= 0.368 Chirality : 0.042 0.336 2298 Planarity : 0.006 0.084 2418 Dihedral : 17.120 95.438 6075 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.61 % Allowed : 11.91 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1638 helix: 0.97 (0.20), residues: 662 sheet: -0.22 (0.30), residues: 256 loop : 0.26 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 332 HIS 0.009 0.001 HIS A 661 PHE 0.021 0.001 PHE A 620 TYR 0.020 0.001 TYR B 681 ARG 0.012 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8879 (mmm) cc_final: 0.8329 (mmm) REVERT: A 414 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6748 (mtm110) REVERT: A 689 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6286 (mtm-85) REVERT: A 786 GLU cc_start: 0.7176 (mp0) cc_final: 0.6968 (pm20) REVERT: A 848 HIS cc_start: 0.7761 (m-70) cc_final: 0.7351 (m90) REVERT: B 145 SER cc_start: 0.8773 (m) cc_final: 0.8562 (m) REVERT: B 594 GLU cc_start: 0.7553 (mp0) cc_final: 0.7226 (mp0) REVERT: B 729 ARG cc_start: 0.8456 (mpp-170) cc_final: 0.8159 (mmt-90) REVERT: B 794 ASP cc_start: 0.7020 (t70) cc_final: 0.6632 (t0) outliers start: 9 outliers final: 4 residues processed: 216 average time/residue: 1.6944 time to fit residues: 394.6231 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 637 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 625 HIS A 638 ASN B 195 GLN B 663 GLN B 848 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14958 Z= 0.292 Angle : 0.577 8.543 20463 Z= 0.299 Chirality : 0.042 0.155 2298 Planarity : 0.005 0.062 2418 Dihedral : 14.750 97.174 2710 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.98 % Allowed : 11.64 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1638 helix: 1.16 (0.20), residues: 654 sheet: -0.61 (0.30), residues: 244 loop : 0.35 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 PHE 0.014 0.002 PHE A 435 TYR 0.021 0.002 TYR B 681 ARG 0.007 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 200 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 219 SER cc_start: 0.8848 (t) cc_final: 0.8645 (p) REVERT: A 385 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: A 482 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6346 (tm-30) REVERT: A 729 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7620 (mtt90) REVERT: A 848 HIS cc_start: 0.7772 (m-70) cc_final: 0.7355 (m90) REVERT: B 11 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: B 38 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7730 (tp40) REVERT: B 198 TYR cc_start: 0.7693 (p90) cc_final: 0.7471 (p90) REVERT: B 428 ASN cc_start: 0.8567 (m-40) cc_final: 0.8283 (m-40) REVERT: B 479 GLN cc_start: 0.8136 (tp40) cc_final: 0.7673 (mp10) REVERT: B 594 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: B 794 ASP cc_start: 0.7021 (t70) cc_final: 0.6586 (t0) outliers start: 44 outliers final: 12 residues processed: 229 average time/residue: 1.5984 time to fit residues: 397.5461 Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 584 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 153 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS B 224 GLN B 420 HIS B 545 GLN B 848 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14958 Z= 0.192 Angle : 0.522 8.610 20463 Z= 0.270 Chirality : 0.040 0.154 2298 Planarity : 0.004 0.043 2418 Dihedral : 14.534 93.039 2705 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.71 % Allowed : 12.65 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1638 helix: 1.29 (0.20), residues: 656 sheet: -0.62 (0.31), residues: 244 loop : 0.39 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 PHE 0.010 0.001 PHE A 435 TYR 0.018 0.001 TYR B 681 ARG 0.014 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: A 200 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: A 335 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: A 351 MET cc_start: 0.8982 (mmm) cc_final: 0.8580 (mmm) REVERT: A 385 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: A 482 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6328 (tm-30) REVERT: A 649 GLU cc_start: 0.7742 (mp0) cc_final: 0.7381 (mp0) REVERT: A 729 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7631 (mtt90) REVERT: A 830 MET cc_start: 0.7687 (tpp) cc_final: 0.7054 (mmm) REVERT: A 848 HIS cc_start: 0.7712 (m-70) cc_final: 0.7325 (m90) REVERT: B 11 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: B 195 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8095 (mm110) REVERT: B 198 TYR cc_start: 0.7668 (p90) cc_final: 0.7447 (p90) REVERT: B 428 ASN cc_start: 0.8568 (m-40) cc_final: 0.8284 (m-40) REVERT: B 479 GLN cc_start: 0.8127 (tp40) cc_final: 0.7617 (mp10) REVERT: B 594 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: B 789 MET cc_start: 0.7019 (tpp) cc_final: 0.6751 (mmp) REVERT: B 794 ASP cc_start: 0.7046 (t70) cc_final: 0.6605 (t0) REVERT: B 808 ASP cc_start: 0.8433 (m-30) cc_final: 0.8167 (m-30) outliers start: 40 outliers final: 14 residues processed: 218 average time/residue: 1.6074 time to fit residues: 380.2766 Evaluate side-chains 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 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 145 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 545 GLN B 848 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14958 Z= 0.227 Angle : 0.521 8.401 20463 Z= 0.268 Chirality : 0.040 0.149 2298 Planarity : 0.005 0.057 2418 Dihedral : 14.437 89.890 2702 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.50 % Allowed : 13.67 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1638 helix: 1.32 (0.20), residues: 658 sheet: -0.62 (0.31), residues: 244 loop : 0.32 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS A 420 PHE 0.011 0.001 PHE A 620 TYR 0.022 0.001 TYR B 681 ARG 0.014 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 200 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: A 335 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: A 414 ARG cc_start: 0.7291 (mtm110) cc_final: 0.7012 (mtm110) REVERT: A 431 MET cc_start: 0.8895 (mmt) cc_final: 0.8491 (mmt) REVERT: A 482 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6346 (tm-30) REVERT: A 649 GLU cc_start: 0.7728 (mp0) cc_final: 0.7359 (mp0) REVERT: A 830 MET cc_start: 0.7674 (tpp) cc_final: 0.7070 (mmm) REVERT: A 848 HIS cc_start: 0.7785 (m-70) cc_final: 0.7269 (m-70) REVERT: B 11 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: B 198 TYR cc_start: 0.7668 (p90) cc_final: 0.7396 (p90) REVERT: B 428 ASN cc_start: 0.8590 (m-40) cc_final: 0.8317 (m-40) REVERT: B 479 GLN cc_start: 0.8090 (tp40) cc_final: 0.7606 (mp10) REVERT: B 594 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: B 794 ASP cc_start: 0.7062 (t70) cc_final: 0.6615 (t0) REVERT: B 808 ASP cc_start: 0.8410 (m-30) cc_final: 0.8099 (m-30) outliers start: 37 outliers final: 14 residues processed: 206 average time/residue: 1.5568 time to fit residues: 348.8684 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 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 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 0.0470 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14958 Z= 0.145 Angle : 0.485 8.189 20463 Z= 0.249 Chirality : 0.039 0.152 2298 Planarity : 0.004 0.039 2418 Dihedral : 14.304 85.377 2702 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.10 % Allowed : 14.88 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1638 helix: 1.54 (0.21), residues: 660 sheet: -0.52 (0.32), residues: 246 loop : 0.37 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 413 HIS 0.008 0.001 HIS A 661 PHE 0.015 0.001 PHE A 620 TYR 0.020 0.001 TYR B 681 ARG 0.010 0.001 ARG A 690 *********************** 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: 31 poor density : 202 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 385 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8183 (mmtm) REVERT: A 482 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6315 (tm-30) REVERT: A 649 GLU cc_start: 0.7747 (mp0) cc_final: 0.7368 (mp0) REVERT: A 830 MET cc_start: 0.7582 (tpp) cc_final: 0.7017 (mmm) REVERT: A 848 HIS cc_start: 0.7779 (m-70) cc_final: 0.7264 (m-70) REVERT: B 198 TYR cc_start: 0.7578 (p90) cc_final: 0.7355 (p90) REVERT: B 479 GLN cc_start: 0.8022 (tp40) cc_final: 0.7549 (mp10) REVERT: B 690 ARG cc_start: 0.6771 (mtm110) cc_final: 0.6503 (mtt90) REVERT: B 794 ASP cc_start: 0.6958 (t70) cc_final: 0.6516 (t0) REVERT: B 808 ASP cc_start: 0.8310 (m-30) cc_final: 0.7895 (m-30) outliers start: 31 outliers final: 12 residues processed: 220 average time/residue: 1.4877 time to fit residues: 356.4654 Evaluate side-chains 196 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 881 VAL 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 452 GLN Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 712 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.7980 chunk 147 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14958 Z= 0.192 Angle : 0.503 7.961 20463 Z= 0.258 Chirality : 0.040 0.149 2298 Planarity : 0.004 0.058 2418 Dihedral : 14.269 83.417 2702 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.83 % Allowed : 16.04 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1638 helix: 1.55 (0.21), residues: 660 sheet: -0.49 (0.32), residues: 246 loop : 0.35 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.008 0.001 HIS A 661 PHE 0.010 0.001 PHE B 435 TYR 0.022 0.001 TYR B 681 ARG 0.017 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: A 212 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8928 (mt) REVERT: A 335 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: A 385 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (mmtm) REVERT: A 414 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6896 (mtm110) REVERT: A 482 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6320 (tm-30) REVERT: A 649 GLU cc_start: 0.7767 (mp0) cc_final: 0.7363 (mp0) REVERT: A 830 MET cc_start: 0.7586 (tpp) cc_final: 0.7301 (mmm) REVERT: A 848 HIS cc_start: 0.7789 (m-70) cc_final: 0.7283 (m-70) REVERT: B 428 ASN cc_start: 0.8492 (m-40) cc_final: 0.8177 (m110) REVERT: B 479 GLN cc_start: 0.8105 (tp40) cc_final: 0.7638 (mp10) REVERT: B 594 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: B 794 ASP cc_start: 0.6977 (t70) cc_final: 0.6526 (t0) REVERT: B 808 ASP cc_start: 0.8292 (m-30) cc_final: 0.7901 (m-30) outliers start: 27 outliers final: 10 residues processed: 203 average time/residue: 1.5856 time to fit residues: 349.9143 Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 212 LEU 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 776 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 294 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 120 optimal weight: 0.0970 chunk 138 optimal weight: 0.0170 chunk 91 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14958 Z= 0.158 Angle : 0.493 7.738 20463 Z= 0.252 Chirality : 0.039 0.150 2298 Planarity : 0.004 0.056 2418 Dihedral : 14.218 82.486 2702 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 15.90 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1638 helix: 1.67 (0.21), residues: 660 sheet: -0.39 (0.32), residues: 246 loop : 0.39 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.006 0.001 HIS A 661 PHE 0.010 0.001 PHE B 435 TYR 0.021 0.001 TYR B 681 ARG 0.013 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 335 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: A 336 ASP cc_start: 0.7083 (m-30) cc_final: 0.6803 (t70) REVERT: A 351 MET cc_start: 0.8874 (mmm) cc_final: 0.8531 (mmm) REVERT: A 385 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (mmtm) REVERT: A 414 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6943 (mtm110) REVERT: A 431 MET cc_start: 0.8728 (mmt) cc_final: 0.8118 (mmp) REVERT: A 482 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6345 (tm-30) REVERT: A 649 GLU cc_start: 0.7751 (mp0) cc_final: 0.7456 (mp0) REVERT: A 830 MET cc_start: 0.7576 (tpp) cc_final: 0.7333 (mmm) REVERT: A 848 HIS cc_start: 0.7825 (m-70) cc_final: 0.7281 (m-70) REVERT: B 291 ARG cc_start: 0.7306 (pmt170) cc_final: 0.7029 (mmm160) REVERT: B 428 ASN cc_start: 0.8418 (m-40) cc_final: 0.8172 (m-40) REVERT: B 479 GLN cc_start: 0.8049 (tp40) cc_final: 0.7532 (mp10) REVERT: B 594 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: B 689 ARG cc_start: 0.6982 (mtm110) cc_final: 0.6684 (mmp80) REVERT: B 690 ARG cc_start: 0.6663 (mtm110) cc_final: 0.6369 (mtt90) REVERT: B 794 ASP cc_start: 0.7090 (t70) cc_final: 0.6647 (t0) REVERT: B 808 ASP cc_start: 0.8225 (m-30) cc_final: 0.7940 (m-30) outliers start: 33 outliers final: 10 residues processed: 210 average time/residue: 1.5373 time to fit residues: 350.6704 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 385 LYS 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 145 SER Chi-restraints excluded: chain B residue 294 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.0020 chunk 149 optimal weight: 0.0030 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14958 Z= 0.156 Angle : 0.490 7.357 20463 Z= 0.251 Chirality : 0.039 0.150 2298 Planarity : 0.004 0.050 2418 Dihedral : 14.183 81.343 2702 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.76 % Allowed : 16.44 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1638 helix: 1.69 (0.21), residues: 662 sheet: -0.42 (0.33), residues: 248 loop : 0.48 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.007 0.001 HIS A 661 PHE 0.011 0.001 PHE B 435 TYR 0.019 0.001 TYR B 681 ARG 0.013 0.001 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: A 336 ASP cc_start: 0.7110 (m-30) cc_final: 0.6832 (t70) REVERT: A 351 MET cc_start: 0.8881 (mmm) cc_final: 0.8483 (mmm) REVERT: A 414 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6962 (mtm110) REVERT: A 431 MET cc_start: 0.8725 (mmt) cc_final: 0.8119 (mmp) REVERT: A 482 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6343 (tm-30) REVERT: A 617 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7449 (ttp-170) REVERT: A 649 GLU cc_start: 0.7780 (mp0) cc_final: 0.7480 (mp0) REVERT: A 848 HIS cc_start: 0.7739 (m-70) cc_final: 0.7274 (m-70) REVERT: B 291 ARG cc_start: 0.7336 (pmt170) cc_final: 0.6960 (mmp80) REVERT: B 428 ASN cc_start: 0.8412 (m-40) cc_final: 0.8161 (m-40) REVERT: B 479 GLN cc_start: 0.8032 (tp40) cc_final: 0.7523 (mp10) REVERT: B 594 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: B 656 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.6688 (ptp90) REVERT: B 689 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6773 (mmp80) REVERT: B 690 ARG cc_start: 0.6753 (mtm110) cc_final: 0.6431 (mtt90) REVERT: B 794 ASP cc_start: 0.6973 (t70) cc_final: 0.6520 (t0) REVERT: B 808 ASP cc_start: 0.8164 (m-30) cc_final: 0.7912 (m-30) outliers start: 26 outliers final: 10 residues processed: 208 average time/residue: 1.5110 time to fit residues: 341.4421 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 0.0980 chunk 152 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 119 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.0670 overall best weight: 0.1918 ------------------------------------------------------------------------------- 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 545 GLN B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14958 Z= 0.140 Angle : 0.491 6.849 20463 Z= 0.251 Chirality : 0.039 0.152 2298 Planarity : 0.004 0.055 2418 Dihedral : 14.143 79.970 2702 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 17.25 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1638 helix: 1.82 (0.21), residues: 662 sheet: -0.32 (0.33), residues: 252 loop : 0.52 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 413 HIS 0.007 0.001 HIS A 661 PHE 0.010 0.001 PHE B 435 TYR 0.017 0.001 TYR A 198 ARG 0.014 0.001 ARG B 414 *********************** 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 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7086 (m-30) cc_final: 0.6820 (t70) REVERT: A 337 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8418 (ptmm) REVERT: A 351 MET cc_start: 0.8787 (mmm) cc_final: 0.8328 (mmm) REVERT: A 414 ARG cc_start: 0.7247 (mtm110) cc_final: 0.6996 (mtm110) REVERT: A 431 MET cc_start: 0.8716 (mmt) cc_final: 0.8110 (mmp) REVERT: A 482 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6372 (tm-30) REVERT: A 590 ARG cc_start: 0.7629 (ttt90) cc_final: 0.7064 (ttp80) REVERT: A 617 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7456 (ttp-170) REVERT: A 649 GLU cc_start: 0.7766 (mp0) cc_final: 0.7499 (mp0) REVERT: A 729 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7137 (mtt90) REVERT: A 848 HIS cc_start: 0.7683 (m-70) cc_final: 0.7396 (m90) REVERT: B 291 ARG cc_start: 0.7299 (pmt170) cc_final: 0.6944 (mmp80) REVERT: B 350 MET cc_start: 0.8984 (mtp) cc_final: 0.8728 (mtm) REVERT: B 479 GLN cc_start: 0.8079 (tp40) cc_final: 0.7509 (mp10) REVERT: B 594 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: B 626 ARG cc_start: 0.6993 (mmp-170) cc_final: 0.6673 (mmp-170) REVERT: B 656 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.6705 (ptp90) REVERT: B 689 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6753 (mmp80) REVERT: B 690 ARG cc_start: 0.6690 (mtm110) cc_final: 0.6348 (mtt90) REVERT: B 794 ASP cc_start: 0.6992 (t70) cc_final: 0.6589 (t0) REVERT: B 808 ASP cc_start: 0.8135 (m-30) cc_final: 0.7885 (m-30) outliers start: 15 outliers final: 8 residues processed: 199 average time/residue: 1.6209 time to fit residues: 351.0052 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU 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 B residue 294 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 479 GLN B 545 GLN B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14958 Z= 0.385 Angle : 0.596 6.921 20463 Z= 0.304 Chirality : 0.043 0.145 2298 Planarity : 0.005 0.065 2418 Dihedral : 14.313 80.354 2702 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.29 % Allowed : 17.32 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1638 helix: 1.40 (0.20), residues: 662 sheet: -0.53 (0.32), residues: 256 loop : 0.35 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.008 0.001 HIS A 661 PHE 0.016 0.002 PHE B 103 TYR 0.029 0.002 TYR B 681 ARG 0.015 0.001 ARG A 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: A 384 LYS cc_start: 0.7244 (mppt) cc_final: 0.6920 (mmtp) REVERT: A 431 MET cc_start: 0.8737 (mmt) cc_final: 0.8322 (mmp) REVERT: A 482 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6356 (tm-30) REVERT: A 649 GLU cc_start: 0.7786 (mp0) cc_final: 0.7457 (mp0) REVERT: A 848 HIS cc_start: 0.7731 (m-70) cc_final: 0.7288 (m-70) REVERT: B 63 MET cc_start: 0.9075 (mtm) cc_final: 0.8783 (mpp) REVERT: B 479 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: B 656 ARG cc_start: 0.6895 (mtm-85) cc_final: 0.6682 (ptp90) REVERT: B 690 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6447 (mtt90) REVERT: B 794 ASP cc_start: 0.7038 (t70) cc_final: 0.6605 (t0) REVERT: B 808 ASP cc_start: 0.8440 (m-30) cc_final: 0.8149 (m-30) outliers start: 19 outliers final: 10 residues processed: 199 average time/residue: 1.6317 time to fit residues: 352.0296 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 397 LEU 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 268 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 675 THR 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 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 479 GLN B 479 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 = 0.3866 r_free = 0.3866 target = 0.167836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122035 restraints weight = 15135.748| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.84 r_work: 0.3076 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14958 Z= 0.233 Angle : 0.550 7.502 20463 Z= 0.281 Chirality : 0.040 0.147 2298 Planarity : 0.005 0.085 2418 Dihedral : 14.291 80.580 2702 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.15 % Allowed : 17.59 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1638 helix: 1.44 (0.20), residues: 662 sheet: -0.58 (0.32), residues: 254 loop : 0.35 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.009 0.001 HIS B 848 PHE 0.018 0.001 PHE B 103 TYR 0.015 0.001 TYR A 198 ARG 0.019 0.001 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5939.50 seconds wall clock time: 107 minutes 31.30 seconds (6451.30 seconds total)