Starting phenix.real_space_refine on Tue Jul 29 19:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.map" model { file = "/net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asj_43816/07_2025/9asj_43816.cif" } resolution = 3.5 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= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 74 5.16 5 C 7434 2.51 5 N 1990 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11626 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 13.63, per 1000 atoms: 1.17 Number of scatterers: 11626 At special positions: 0 Unit cell: (96.6, 155.48, 83.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 6 15.00 O 2122 8.00 N 1990 7.00 C 7434 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 57.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.218A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.897A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.558A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.532A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.894A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 367 removed outlier: 3.656A pdb=" N TYR A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.837A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.876A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.584A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.892A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.924A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.710A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.596A pdb=" N SER A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.524A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 679 through 687 removed outlier: 3.506A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.709A pdb=" N ILE A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.909A pdb=" N LEU A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.504A pdb=" N GLU A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 776 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.627A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.525A pdb=" N ARG A 798 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 799 " --> pdb=" O LEU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.545A pdb=" N ARG A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.904A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.706A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.218A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.897A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.558A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.532A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.894A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 removed outlier: 3.655A pdb=" N TYR B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.836A pdb=" N ARG B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.877A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 421 through 434 Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.584A pdb=" N SER B 448 " --> pdb=" O THR B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.893A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.924A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.710A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.596A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.524A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 679 through 687 removed outlier: 3.507A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 730 removed outlier: 3.710A pdb=" N ILE B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.909A pdb=" N LEU B 751 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.504A pdb=" N GLU B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 776 " --> pdb=" O HIS B 772 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 787 removed outlier: 3.628A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.525A pdb=" N ARG B 798 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 799 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 795 through 799' Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.545A pdb=" N ARG B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.903A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.707A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 7.070A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 214 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 311 removed outlier: 7.536A pdb=" N ILE A 302 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 492 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 297 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.069A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS B 139 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 212 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 214 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 311 removed outlier: 7.536A pdb=" N ILE B 302 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 492 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 297 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 Processing sheet with id=AB1, first strand: chain 'B' and resid 862 through 863 556 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3768 1.34 - 1.46: 2622 1.46 - 1.58: 5310 1.58 - 1.70: 8 1.70 - 1.82: 122 Bond restraints: 11830 Sorted by residual: bond pdb=" C2' ANP A 901 " pdb=" C3' ANP A 901 " ideal model delta sigma weight residual 1.520 1.292 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' ANP B 901 " pdb=" C3' ANP B 901 " ideal model delta sigma weight residual 1.520 1.292 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C6 ANP A 901 " pdb=" N6 ANP A 901 " ideal model delta sigma weight residual 1.340 1.491 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 ANP B 901 " pdb=" N6 ANP B 901 " ideal model delta sigma weight residual 1.340 1.491 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C1' ANP B 901 " pdb=" O4' ANP B 901 " ideal model delta sigma weight residual 1.394 1.514 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 11825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 15739 2.24 - 4.48: 207 4.48 - 6.72: 39 6.72 - 8.95: 21 8.95 - 11.19: 10 Bond angle restraints: 16016 Sorted by residual: angle pdb=" O3A ANP A 901 " pdb=" PA ANP A 901 " pdb=" O5' ANP A 901 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O3A ANP B 901 " pdb=" PA ANP B 901 " pdb=" O5' ANP B 901 " ideal model delta sigma weight residual 98.09 109.25 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB MET B 885 " pdb=" CG MET B 885 " pdb=" SD MET B 885 " ideal model delta sigma weight residual 112.70 123.81 -11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CB MET A 885 " pdb=" CG MET A 885 " pdb=" SD MET A 885 " ideal model delta sigma weight residual 112.70 123.78 -11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.67 10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 16011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5879 17.09 - 34.18: 879 34.18 - 51.27: 296 51.27 - 68.36: 58 68.36 - 85.45: 28 Dihedral angle restraints: 7140 sinusoidal: 2854 harmonic: 4286 Sorted by residual: dihedral pdb=" CG ARG A 637 " pdb=" CD ARG A 637 " pdb=" NE ARG A 637 " pdb=" CZ ARG A 637 " ideal model delta sinusoidal sigma weight residual -180.00 -136.23 -43.77 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 637 " pdb=" CD ARG B 637 " pdb=" NE ARG B 637 " pdb=" CZ ARG B 637 " ideal model delta sinusoidal sigma weight residual -180.00 -136.29 -43.71 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP A 630 " pdb=" CB ASP A 630 " pdb=" CG ASP A 630 " pdb=" OD1 ASP A 630 " ideal model delta sinusoidal sigma weight residual -30.00 -84.55 54.55 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 7137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1729 0.069 - 0.138: 147 0.138 - 0.207: 6 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C2' ANP B 901 " pdb=" C1' ANP B 901 " pdb=" C3' ANP B 901 " pdb=" O2' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.38 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C2' ANP A 901 " pdb=" C1' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" O2' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.38 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C4' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" C5' ANP A 901 " pdb=" O4' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1881 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 290 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 291 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 290 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO A 291 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 397 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 398 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " -0.023 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 513 2.73 - 3.27: 11971 3.27 - 3.81: 19118 3.81 - 4.36: 22808 4.36 - 4.90: 38879 Nonbonded interactions: 93289 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" OH TYR A 283 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU B 98 " pdb=" OH TYR B 283 " model vdw 2.184 3.040 nonbonded pdb=" NZ LYS B 109 " pdb=" OD1 ASN B 279 " model vdw 2.236 3.120 nonbonded pdb=" NZ LYS A 109 " pdb=" OD1 ASN A 279 " model vdw 2.236 3.120 nonbonded pdb=" O ALA A 617 " pdb=" OG SER A 621 " model vdw 2.240 3.040 ... (remaining 93284 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.730 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 0.228 11830 Z= 0.270 Angle : 0.706 11.192 16016 Z= 0.315 Chirality : 0.041 0.345 1884 Planarity : 0.004 0.064 1992 Dihedral : 18.824 85.447 4356 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.24 % Allowed : 34.42 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.22), residues: 1446 helix: -0.41 (0.19), residues: 758 sheet: 0.33 (0.46), residues: 126 loop : -1.10 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 411 HIS 0.004 0.001 HIS A 610 PHE 0.012 0.001 PHE A 313 TYR 0.012 0.001 TYR A 239 ARG 0.006 0.000 ARG B 798 Details of bonding type rmsd hydrogen bonds : bond 0.26815 ( 556) hydrogen bonds : angle 7.93797 ( 1596) covalent geometry : bond 0.00549 (11830) covalent geometry : angle 0.70555 (16016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 1.327 Fit side-chains REVERT: A 639 MET cc_start: 0.4324 (mmp) cc_final: 0.4011 (mmp) REVERT: B 639 MET cc_start: 0.4339 (mmp) cc_final: 0.4026 (mmp) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.2346 time to fit residues: 68.4700 Evaluate side-chains 158 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 498 ASN A 551 HIS A 610 HIS A 753 GLN B 300 ASN B 451 ASN B 498 ASN B 551 HIS B 610 HIS B 753 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141264 restraints weight = 16900.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146474 restraints weight = 9073.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150163 restraints weight = 6015.399| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11830 Z= 0.132 Angle : 0.631 10.007 16016 Z= 0.310 Chirality : 0.041 0.155 1884 Planarity : 0.004 0.051 1992 Dihedral : 8.136 75.602 1644 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.63 % Allowed : 30.67 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.22), residues: 1446 helix: 0.13 (0.18), residues: 794 sheet: 0.47 (0.45), residues: 130 loop : -1.36 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 411 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE B 670 TYR 0.011 0.002 TYR B 113 ARG 0.006 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 556) hydrogen bonds : angle 5.15942 ( 1596) covalent geometry : bond 0.00297 (11830) covalent geometry : angle 0.63144 (16016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7311 (tptt) cc_final: 0.6720 (pttt) REVERT: A 146 PHE cc_start: 0.8211 (m-80) cc_final: 0.7932 (m-80) REVERT: A 639 MET cc_start: 0.4617 (mmp) cc_final: 0.3950 (mmp) REVERT: A 680 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6861 (mpp) REVERT: A 741 TYR cc_start: 0.7390 (m-80) cc_final: 0.6854 (m-80) REVERT: B 639 MET cc_start: 0.4572 (mmp) cc_final: 0.3890 (mmp) REVERT: B 680 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6854 (mpp) REVERT: B 741 TYR cc_start: 0.7531 (m-80) cc_final: 0.6945 (m-80) outliers start: 58 outliers final: 33 residues processed: 223 average time/residue: 0.2015 time to fit residues: 67.3409 Evaluate side-chains 192 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 68 optimal weight: 0.0370 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 649 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 649 HIS ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139218 restraints weight = 17160.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144436 restraints weight = 9267.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148113 restraints weight = 6170.509| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11830 Z= 0.146 Angle : 0.606 9.499 16016 Z= 0.300 Chirality : 0.041 0.163 1884 Planarity : 0.004 0.052 1992 Dihedral : 7.950 72.641 1644 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.47 % Allowed : 30.83 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.22), residues: 1446 helix: 0.16 (0.18), residues: 806 sheet: 0.37 (0.44), residues: 130 loop : -1.39 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 411 HIS 0.005 0.001 HIS B 649 PHE 0.012 0.001 PHE A 432 TYR 0.012 0.002 TYR A 171 ARG 0.004 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 556) hydrogen bonds : angle 4.79497 ( 1596) covalent geometry : bond 0.00346 (11830) covalent geometry : angle 0.60632 (16016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8225 (m-80) cc_final: 0.7951 (m-80) REVERT: A 152 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: A 300 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 344 CYS cc_start: 0.8352 (m) cc_final: 0.8108 (p) REVERT: A 639 MET cc_start: 0.4878 (mmp) cc_final: 0.4092 (mmp) REVERT: A 680 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: A 741 TYR cc_start: 0.7561 (m-80) cc_final: 0.6995 (m-80) REVERT: A 775 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6859 (tt0) REVERT: A 888 GLN cc_start: 0.7824 (tp40) cc_final: 0.7301 (tt0) REVERT: B 152 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: B 216 ASP cc_start: 0.7620 (t0) cc_final: 0.7287 (t0) REVERT: B 300 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7973 (t0) REVERT: B 344 CYS cc_start: 0.8341 (m) cc_final: 0.8128 (p) REVERT: B 531 MET cc_start: 0.7003 (tpt) cc_final: 0.6800 (tpt) REVERT: B 550 MET cc_start: 0.6170 (tmm) cc_final: 0.5954 (tmm) REVERT: B 639 MET cc_start: 0.4795 (mmp) cc_final: 0.4035 (mmp) REVERT: B 680 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: B 741 TYR cc_start: 0.7556 (m-80) cc_final: 0.6939 (m-80) REVERT: B 775 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6882 (tt0) outliers start: 56 outliers final: 33 residues processed: 211 average time/residue: 0.2002 time to fit residues: 65.1375 Evaluate side-chains 193 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138445 restraints weight = 17198.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143624 restraints weight = 9234.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147208 restraints weight = 6132.274| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11830 Z= 0.146 Angle : 0.597 9.518 16016 Z= 0.294 Chirality : 0.041 0.154 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.827 72.438 1644 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.83 % Allowed : 29.87 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.22), residues: 1446 helix: 0.24 (0.18), residues: 804 sheet: 0.13 (0.44), residues: 130 loop : -1.41 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 411 HIS 0.004 0.001 HIS A 417 PHE 0.011 0.001 PHE A 432 TYR 0.014 0.002 TYR B 113 ARG 0.005 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 556) hydrogen bonds : angle 4.61685 ( 1596) covalent geometry : bond 0.00349 (11830) covalent geometry : angle 0.59694 (16016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 167 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7720 (p0) REVERT: A 146 PHE cc_start: 0.8256 (m-80) cc_final: 0.7973 (m-80) REVERT: A 152 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: A 300 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7897 (t0) REVERT: A 344 CYS cc_start: 0.8476 (m) cc_final: 0.8195 (p) REVERT: A 361 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4013 (t80) REVERT: A 550 MET cc_start: 0.6116 (tmm) cc_final: 0.5582 (tmm) REVERT: A 587 MET cc_start: 0.8083 (tpt) cc_final: 0.7617 (tmm) REVERT: A 639 MET cc_start: 0.4659 (mmp) cc_final: 0.4437 (mmp) REVERT: A 680 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7393 (mpp) REVERT: A 775 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6697 (tt0) REVERT: A 888 GLN cc_start: 0.7862 (tp40) cc_final: 0.7348 (tt0) REVERT: B 110 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 152 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: B 300 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7885 (t0) REVERT: B 344 CYS cc_start: 0.8479 (m) cc_final: 0.8211 (p) REVERT: B 361 PHE cc_start: 0.5124 (OUTLIER) cc_final: 0.3942 (t80) REVERT: B 639 MET cc_start: 0.4680 (mmp) cc_final: 0.4458 (mmp) REVERT: B 680 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7395 (mpp) REVERT: B 775 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6699 (tt0) REVERT: B 888 GLN cc_start: 0.7884 (tp40) cc_final: 0.7359 (tt0) outliers start: 73 outliers final: 49 residues processed: 220 average time/residue: 0.1968 time to fit residues: 65.4820 Evaluate side-chains 215 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 753 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136966 restraints weight = 17133.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142044 restraints weight = 9302.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145568 restraints weight = 6232.879| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11830 Z= 0.158 Angle : 0.622 9.805 16016 Z= 0.303 Chirality : 0.041 0.150 1884 Planarity : 0.004 0.054 1992 Dihedral : 7.732 72.084 1644 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.71 % Rotamer: Outliers : 5.67 % Allowed : 30.35 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.22), residues: 1446 helix: 0.26 (0.18), residues: 806 sheet: -0.00 (0.43), residues: 130 loop : -1.42 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 411 HIS 0.005 0.001 HIS A 417 PHE 0.009 0.001 PHE B 632 TYR 0.012 0.001 TYR A 283 ARG 0.005 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 556) hydrogen bonds : angle 4.54943 ( 1596) covalent geometry : bond 0.00380 (11830) covalent geometry : angle 0.62197 (16016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 165 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 146 PHE cc_start: 0.8317 (m-80) cc_final: 0.8027 (m-80) REVERT: A 152 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: A 300 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7760 (t0) REVERT: A 344 CYS cc_start: 0.8492 (m) cc_final: 0.8199 (p) REVERT: A 550 MET cc_start: 0.6191 (tmm) cc_final: 0.5594 (tmm) REVERT: A 587 MET cc_start: 0.8054 (tpt) cc_final: 0.7647 (tmm) REVERT: A 680 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7440 (mpp) REVERT: A 775 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6272 (tm-30) REVERT: A 888 GLN cc_start: 0.7831 (tp40) cc_final: 0.7370 (tt0) REVERT: B 110 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7752 (p0) REVERT: B 130 LEU cc_start: 0.8635 (mt) cc_final: 0.8416 (mt) REVERT: B 152 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: B 300 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7766 (t0) REVERT: B 344 CYS cc_start: 0.8479 (m) cc_final: 0.8189 (p) REVERT: B 550 MET cc_start: 0.6246 (tmm) cc_final: 0.5683 (tmm) REVERT: B 587 MET cc_start: 0.8071 (tpt) cc_final: 0.7622 (tmm) REVERT: B 680 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7459 (mpp) REVERT: B 741 TYR cc_start: 0.7608 (m-80) cc_final: 0.6806 (m-80) REVERT: B 775 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6260 (tm-30) REVERT: B 888 GLN cc_start: 0.7855 (tp40) cc_final: 0.7373 (tt0) outliers start: 71 outliers final: 49 residues processed: 219 average time/residue: 0.2078 time to fit residues: 68.2765 Evaluate side-chains 206 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 792 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139311 restraints weight = 17206.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144530 restraints weight = 9193.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148079 restraints weight = 6092.705| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11830 Z= 0.125 Angle : 0.603 10.040 16016 Z= 0.295 Chirality : 0.040 0.149 1884 Planarity : 0.004 0.054 1992 Dihedral : 7.608 71.670 1644 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 5.11 % Allowed : 30.59 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.22), residues: 1446 helix: 0.44 (0.18), residues: 798 sheet: 0.05 (0.44), residues: 130 loop : -1.36 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.011 0.001 PHE A 670 TYR 0.014 0.002 TYR A 171 ARG 0.006 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 556) hydrogen bonds : angle 4.42320 ( 1596) covalent geometry : bond 0.00295 (11830) covalent geometry : angle 0.60290 (16016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8313 (m-80) cc_final: 0.8026 (m-80) REVERT: A 152 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: A 300 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7751 (t0) REVERT: A 344 CYS cc_start: 0.8522 (m) cc_final: 0.8212 (p) REVERT: A 361 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4245 (t80) REVERT: A 550 MET cc_start: 0.6268 (tmm) cc_final: 0.5666 (tmm) REVERT: A 587 MET cc_start: 0.8034 (tpt) cc_final: 0.7660 (tmm) REVERT: A 729 ILE cc_start: 0.7856 (pt) cc_final: 0.7325 (mm) REVERT: A 775 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6208 (tm-30) REVERT: A 888 GLN cc_start: 0.7853 (tp40) cc_final: 0.7394 (tt0) REVERT: B 130 LEU cc_start: 0.8614 (mt) cc_final: 0.8388 (mt) REVERT: B 152 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: B 300 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7744 (t0) REVERT: B 344 CYS cc_start: 0.8494 (m) cc_final: 0.8206 (p) REVERT: B 361 PHE cc_start: 0.5185 (OUTLIER) cc_final: 0.4199 (t80) REVERT: B 550 MET cc_start: 0.6278 (tmm) cc_final: 0.5701 (tmm) REVERT: B 587 MET cc_start: 0.8030 (tpt) cc_final: 0.7618 (tmm) REVERT: B 680 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7257 (mpp) REVERT: B 729 ILE cc_start: 0.7859 (pt) cc_final: 0.7468 (mm) REVERT: B 775 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6203 (tm-30) REVERT: B 815 PHE cc_start: 0.8020 (m-80) cc_final: 0.7631 (m-80) REVERT: B 888 GLN cc_start: 0.7856 (tp40) cc_final: 0.7378 (tt0) outliers start: 64 outliers final: 43 residues processed: 219 average time/residue: 0.2117 time to fit residues: 70.4110 Evaluate side-chains 208 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.172548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138620 restraints weight = 17313.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143787 restraints weight = 9297.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147364 restraints weight = 6182.334| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11830 Z= 0.140 Angle : 0.635 12.397 16016 Z= 0.305 Chirality : 0.041 0.147 1884 Planarity : 0.004 0.052 1992 Dihedral : 7.558 70.994 1644 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.88 % Favored : 93.98 % Rotamer: Outliers : 4.71 % Allowed : 31.87 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.22), residues: 1446 helix: 0.49 (0.19), residues: 798 sheet: 0.03 (0.44), residues: 130 loop : -1.42 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.009 0.001 PHE A 670 TYR 0.012 0.002 TYR A 283 ARG 0.005 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 556) hydrogen bonds : angle 4.39950 ( 1596) covalent geometry : bond 0.00336 (11830) covalent geometry : angle 0.63536 (16016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8643 (mt) cc_final: 0.8391 (mt) REVERT: A 146 PHE cc_start: 0.8330 (m-80) cc_final: 0.8058 (m-80) REVERT: A 152 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: A 300 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7798 (t0) REVERT: A 344 CYS cc_start: 0.8519 (m) cc_final: 0.8231 (p) REVERT: A 550 MET cc_start: 0.6364 (tmm) cc_final: 0.5751 (tmm) REVERT: A 587 MET cc_start: 0.8034 (tpt) cc_final: 0.7670 (tmm) REVERT: A 680 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7354 (mpp) REVERT: A 729 ILE cc_start: 0.7802 (pt) cc_final: 0.7319 (mm) REVERT: A 741 TYR cc_start: 0.7115 (m-80) cc_final: 0.6575 (m-80) REVERT: A 775 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6382 (tm-30) REVERT: A 873 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7626 (tpp80) REVERT: A 888 GLN cc_start: 0.7832 (tp40) cc_final: 0.7395 (tt0) REVERT: B 130 LEU cc_start: 0.8629 (mt) cc_final: 0.8394 (mt) REVERT: B 152 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: B 300 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7808 (t0) REVERT: B 344 CYS cc_start: 0.8467 (m) cc_final: 0.8196 (p) REVERT: B 550 MET cc_start: 0.6319 (tmm) cc_final: 0.5739 (tmm) REVERT: B 587 MET cc_start: 0.8053 (tpt) cc_final: 0.7657 (tmm) REVERT: B 680 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7424 (mpp) REVERT: B 729 ILE cc_start: 0.7694 (pt) cc_final: 0.7339 (mm) REVERT: B 775 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6347 (tm-30) REVERT: B 873 ARG cc_start: 0.8402 (ttp80) cc_final: 0.7624 (tpp80) REVERT: B 888 GLN cc_start: 0.7866 (tp40) cc_final: 0.7407 (tt0) outliers start: 59 outliers final: 47 residues processed: 208 average time/residue: 0.1927 time to fit residues: 61.1920 Evaluate side-chains 209 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140302 restraints weight = 17093.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145437 restraints weight = 9183.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149084 restraints weight = 6115.220| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11830 Z= 0.121 Angle : 0.613 11.908 16016 Z= 0.292 Chirality : 0.040 0.160 1884 Planarity : 0.004 0.051 1992 Dihedral : 7.423 69.636 1644 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 4.47 % Allowed : 31.79 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.22), residues: 1446 helix: 0.55 (0.19), residues: 798 sheet: 0.15 (0.45), residues: 130 loop : -1.42 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 277 HIS 0.003 0.001 HIS B 416 PHE 0.013 0.001 PHE A 87 TYR 0.011 0.001 TYR A 171 ARG 0.005 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 556) hydrogen bonds : angle 4.34524 ( 1596) covalent geometry : bond 0.00285 (11830) covalent geometry : angle 0.61284 (16016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8649 (mt) cc_final: 0.8384 (mt) REVERT: A 146 PHE cc_start: 0.8389 (m-80) cc_final: 0.8128 (m-80) REVERT: A 152 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: A 300 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7852 (t0) REVERT: A 344 CYS cc_start: 0.8514 (m) cc_final: 0.8221 (p) REVERT: A 550 MET cc_start: 0.6411 (tmm) cc_final: 0.5838 (tmm) REVERT: A 587 MET cc_start: 0.7987 (tpt) cc_final: 0.7628 (tmm) REVERT: A 680 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: A 729 ILE cc_start: 0.7757 (pt) cc_final: 0.7338 (mm) REVERT: A 741 TYR cc_start: 0.6999 (m-80) cc_final: 0.6532 (m-80) REVERT: A 775 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 888 GLN cc_start: 0.7856 (tp40) cc_final: 0.7442 (tt0) REVERT: B 130 LEU cc_start: 0.8625 (mt) cc_final: 0.8369 (mt) REVERT: B 152 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: B 300 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7870 (t0) REVERT: B 344 CYS cc_start: 0.8532 (m) cc_final: 0.8256 (p) REVERT: B 361 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4366 (t80) REVERT: B 396 ARG cc_start: 0.7011 (ptt90) cc_final: 0.5745 (mmt90) REVERT: B 531 MET cc_start: 0.6937 (tpt) cc_final: 0.6734 (tpt) REVERT: B 550 MET cc_start: 0.6318 (tmm) cc_final: 0.5745 (tmm) REVERT: B 587 MET cc_start: 0.8016 (tpt) cc_final: 0.7658 (tmm) REVERT: B 680 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7245 (mpp) REVERT: B 729 ILE cc_start: 0.7682 (pt) cc_final: 0.7397 (mm) REVERT: B 741 TYR cc_start: 0.6907 (m-80) cc_final: 0.6376 (m-80) REVERT: B 775 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6561 (tm-30) REVERT: B 815 PHE cc_start: 0.8019 (m-80) cc_final: 0.7650 (m-80) REVERT: B 888 GLN cc_start: 0.7873 (tp40) cc_final: 0.7446 (tt0) outliers start: 56 outliers final: 41 residues processed: 201 average time/residue: 0.1831 time to fit residues: 57.6167 Evaluate side-chains 199 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.173757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139767 restraints weight = 17064.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.144912 restraints weight = 9217.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148484 restraints weight = 6168.294| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11830 Z= 0.128 Angle : 0.626 11.765 16016 Z= 0.298 Chirality : 0.041 0.205 1884 Planarity : 0.004 0.051 1992 Dihedral : 7.335 68.238 1644 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.74 % Favored : 94.12 % Rotamer: Outliers : 4.15 % Allowed : 32.51 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.22), residues: 1446 helix: 0.55 (0.19), residues: 798 sheet: 0.08 (0.45), residues: 128 loop : -1.37 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 277 HIS 0.005 0.001 HIS B 417 PHE 0.012 0.001 PHE B 432 TYR 0.011 0.001 TYR A 171 ARG 0.004 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 556) hydrogen bonds : angle 4.36616 ( 1596) covalent geometry : bond 0.00305 (11830) covalent geometry : angle 0.62611 (16016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8646 (mt) cc_final: 0.8365 (mt) REVERT: A 146 PHE cc_start: 0.8346 (m-80) cc_final: 0.8088 (m-80) REVERT: A 300 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7837 (t0) REVERT: A 344 CYS cc_start: 0.8512 (m) cc_final: 0.8214 (p) REVERT: A 361 PHE cc_start: 0.5294 (OUTLIER) cc_final: 0.4415 (t80) REVERT: A 550 MET cc_start: 0.6400 (tmm) cc_final: 0.5808 (tmm) REVERT: A 587 MET cc_start: 0.7991 (tpt) cc_final: 0.7650 (tmm) REVERT: A 680 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7276 (mpp) REVERT: A 729 ILE cc_start: 0.7743 (pt) cc_final: 0.7315 (mm) REVERT: A 741 TYR cc_start: 0.6928 (m-80) cc_final: 0.6494 (m-80) REVERT: A 775 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6649 (tm-30) REVERT: A 873 ARG cc_start: 0.8376 (ttp80) cc_final: 0.7661 (tpp80) REVERT: A 888 GLN cc_start: 0.7885 (tp40) cc_final: 0.7471 (tt0) REVERT: B 130 LEU cc_start: 0.8628 (mt) cc_final: 0.8361 (mt) REVERT: B 300 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.7888 (t0) REVERT: B 344 CYS cc_start: 0.8559 (m) cc_final: 0.8265 (p) REVERT: B 361 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.4386 (t80) REVERT: B 396 ARG cc_start: 0.7002 (ptt90) cc_final: 0.5743 (mmt90) REVERT: B 550 MET cc_start: 0.6251 (tmm) cc_final: 0.5678 (tmm) REVERT: B 587 MET cc_start: 0.8020 (tpt) cc_final: 0.7663 (tmm) REVERT: B 680 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7287 (mpp) REVERT: B 729 ILE cc_start: 0.7640 (pt) cc_final: 0.7346 (mm) REVERT: B 741 TYR cc_start: 0.6948 (m-80) cc_final: 0.6417 (m-80) REVERT: B 775 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6637 (tm-30) REVERT: B 815 PHE cc_start: 0.8014 (m-80) cc_final: 0.7649 (m-80) REVERT: B 873 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7731 (tpp80) REVERT: B 888 GLN cc_start: 0.7891 (tp40) cc_final: 0.7514 (tt0) outliers start: 52 outliers final: 42 residues processed: 193 average time/residue: 0.1869 time to fit residues: 55.4068 Evaluate side-chains 198 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 104 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.175341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.141505 restraints weight = 16934.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.146751 restraints weight = 9069.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150393 restraints weight = 6016.487| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11830 Z= 0.113 Angle : 0.619 11.742 16016 Z= 0.296 Chirality : 0.040 0.187 1884 Planarity : 0.004 0.052 1992 Dihedral : 7.191 66.433 1644 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 3.51 % Allowed : 33.15 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.22), residues: 1446 helix: 0.58 (0.19), residues: 800 sheet: 0.18 (0.45), residues: 128 loop : -1.38 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.023 0.001 PHE B 87 TYR 0.011 0.001 TYR A 171 ARG 0.007 0.000 ARG B 745 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 556) hydrogen bonds : angle 4.34423 ( 1596) covalent geometry : bond 0.00262 (11830) covalent geometry : angle 0.61853 (16016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8648 (mt) cc_final: 0.8371 (mt) REVERT: A 146 PHE cc_start: 0.8277 (m-80) cc_final: 0.8030 (m-80) REVERT: A 344 CYS cc_start: 0.8495 (m) cc_final: 0.8200 (p) REVERT: A 440 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7097 (tp) REVERT: A 550 MET cc_start: 0.6388 (tmm) cc_final: 0.5836 (tmm) REVERT: A 587 MET cc_start: 0.8015 (tpt) cc_final: 0.7661 (tmm) REVERT: A 680 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: A 729 ILE cc_start: 0.7725 (pt) cc_final: 0.7301 (mm) REVERT: A 741 TYR cc_start: 0.6672 (m-80) cc_final: 0.6199 (m-80) REVERT: A 775 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6592 (tm-30) REVERT: A 873 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7665 (tpp80) REVERT: B 130 LEU cc_start: 0.8615 (mt) cc_final: 0.8339 (mt) REVERT: B 300 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.7917 (t0) REVERT: B 344 CYS cc_start: 0.8565 (m) cc_final: 0.8250 (p) REVERT: B 550 MET cc_start: 0.6296 (tmm) cc_final: 0.5776 (tmm) REVERT: B 587 MET cc_start: 0.8011 (tpt) cc_final: 0.7657 (tmm) REVERT: B 680 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7093 (mpp) REVERT: B 729 ILE cc_start: 0.7671 (pt) cc_final: 0.7415 (mm) REVERT: B 741 TYR cc_start: 0.6569 (m-80) cc_final: 0.6057 (m-80) REVERT: B 775 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6570 (tm-30) REVERT: B 815 PHE cc_start: 0.8000 (m-80) cc_final: 0.7653 (m-80) REVERT: B 873 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7732 (tpp80) outliers start: 44 outliers final: 37 residues processed: 190 average time/residue: 0.1995 time to fit residues: 59.0425 Evaluate side-chains 192 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 87 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.174313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140452 restraints weight = 17017.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145614 restraints weight = 9126.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149242 restraints weight = 6055.683| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11830 Z= 0.128 Angle : 0.638 11.529 16016 Z= 0.305 Chirality : 0.041 0.182 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.101 64.804 1644 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.60 % Favored : 94.26 % Rotamer: Outliers : 3.51 % Allowed : 33.31 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.22), residues: 1446 helix: 0.57 (0.19), residues: 800 sheet: 0.12 (0.45), residues: 128 loop : -1.36 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.029 0.001 PHE A 87 TYR 0.011 0.001 TYR A 113 ARG 0.007 0.000 ARG B 745 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 556) hydrogen bonds : angle 4.40728 ( 1596) covalent geometry : bond 0.00306 (11830) covalent geometry : angle 0.63807 (16016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3755.48 seconds wall clock time: 66 minutes 8.85 seconds (3968.85 seconds total)