Starting phenix.real_space_refine on Sat Aug 23 11:02:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asj_43816/08_2025/9asj_43816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asj_43816/08_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_43816/08_2025/9asj_43816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asj_43816/08_2025/9asj_43816.map" model { file = "/net/cci-nas-00/data/ceres_data/9asj_43816/08_2025/9asj_43816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asj_43816/08_2025/9asj_43816.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} 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: 4.26, per 1000 atoms: 0.37 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: 0.94 Conformation dependent library (CDL) restraints added in 556.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.49 Time building geometry restraints manager: 1.17 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: 0.01 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: 3.280 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- 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 : 13.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.22), 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 ARG 0.006 0.000 ARG B 798 TYR 0.012 0.001 TYR A 239 PHE 0.012 0.001 PHE A 313 TRP 0.017 0.001 TRP B 411 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00549 (11830) covalent geometry : angle 0.70555 (16016) hydrogen bonds : bond 0.26815 ( 556) hydrogen bonds : angle 7.93797 ( 1596) *********************** 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 : 0.439 Fit side-chains REVERT: A 639 MET cc_start: 0.4324 (mmp) cc_final: 0.4010 (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: 0.0886 time to fit residues: 26.4759 Evaluate side-chains 160 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.173717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140181 restraints weight = 17027.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145404 restraints weight = 9174.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.149042 restraints weight = 6097.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151558 restraints weight = 4609.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.153301 restraints weight = 3791.173| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1660 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= 0.144 Angle : 0.637 9.965 16016 Z= 0.314 Chirality : 0.041 0.152 1884 Planarity : 0.004 0.052 1992 Dihedral : 8.151 75.693 1644 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.63 % Allowed : 31.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.22), residues: 1446 helix: 0.09 (0.18), residues: 794 sheet: 0.41 (0.44), residues: 130 loop : -1.35 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 226 TYR 0.011 0.001 TYR B 113 PHE 0.014 0.001 PHE B 670 TRP 0.016 0.001 TRP B 411 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00323 (11830) covalent geometry : angle 0.63745 (16016) hydrogen bonds : bond 0.04445 ( 556) hydrogen bonds : angle 5.16315 ( 1596) *********************** 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 : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7280 (tptt) cc_final: 0.6677 (pttt) REVERT: A 146 PHE cc_start: 0.8219 (m-80) cc_final: 0.7925 (m-80) REVERT: A 639 MET cc_start: 0.4542 (mmp) cc_final: 0.3874 (mmp) REVERT: A 680 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6926 (mpp) REVERT: A 741 TYR cc_start: 0.7382 (m-80) cc_final: 0.6860 (m-80) REVERT: B 639 MET cc_start: 0.4489 (mmp) cc_final: 0.3805 (mmp) REVERT: B 680 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6922 (mpp) REVERT: B 741 TYR cc_start: 0.7542 (m-80) cc_final: 0.6938 (m-80) outliers start: 58 outliers final: 33 residues processed: 223 average time/residue: 0.0785 time to fit residues: 26.4853 Evaluate side-chains 194 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 450 VAL 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 450 VAL 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 69 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.174008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140241 restraints weight = 17326.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145532 restraints weight = 9252.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149270 restraints weight = 6118.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151812 restraints weight = 4603.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153561 restraints weight = 3782.932| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11830 Z= 0.133 Angle : 0.601 9.314 16016 Z= 0.297 Chirality : 0.041 0.172 1884 Planarity : 0.004 0.050 1992 Dihedral : 7.922 72.504 1644 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.31 % Allowed : 30.11 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.22), residues: 1446 helix: 0.18 (0.18), residues: 802 sheet: 0.48 (0.45), residues: 130 loop : -1.46 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.013 0.002 TYR B 652 PHE 0.009 0.001 PHE A 670 TRP 0.021 0.001 TRP B 411 HIS 0.005 0.001 HIS A 649 Details of bonding type rmsd covalent geometry : bond 0.00310 (11830) covalent geometry : angle 0.60071 (16016) hydrogen bonds : bond 0.03878 ( 556) hydrogen bonds : angle 4.79165 ( 1596) *********************** 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 234 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8213 (m-80) cc_final: 0.7944 (m-80) REVERT: A 300 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7965 (t0) REVERT: A 344 CYS cc_start: 0.8256 (m) cc_final: 0.8045 (p) REVERT: A 639 MET cc_start: 0.4689 (mmp) cc_final: 0.3960 (mmp) REVERT: A 680 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7104 (mpp) REVERT: A 741 TYR cc_start: 0.7536 (m-80) cc_final: 0.7062 (m-80) REVERT: A 775 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6854 (tt0) REVERT: A 888 GLN cc_start: 0.7758 (tp40) cc_final: 0.7367 (tt0) REVERT: B 146 PHE cc_start: 0.8259 (m-80) cc_final: 0.7980 (m-80) REVERT: B 152 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7859 (tp30) REVERT: B 300 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7883 (t0) REVERT: B 531 MET cc_start: 0.6994 (tpt) cc_final: 0.6790 (tpt) REVERT: B 550 MET cc_start: 0.6263 (tmm) cc_final: 0.6054 (tmm) REVERT: B 639 MET cc_start: 0.4706 (mmp) cc_final: 0.3977 (mmp) REVERT: B 680 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7081 (mpp) REVERT: B 741 TYR cc_start: 0.7505 (m-80) cc_final: 0.6996 (m-80) REVERT: B 888 GLN cc_start: 0.7794 (tp40) cc_final: 0.7337 (tt0) outliers start: 54 outliers final: 28 residues processed: 217 average time/residue: 0.0796 time to fit residues: 26.8218 Evaluate side-chains 192 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 390 VAL 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 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 360 GLU Chi-restraints excluded: chain B residue 390 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: 0.5980 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 0.0060 chunk 116 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 21 optimal weight: 0.0000 chunk 140 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137968 restraints weight = 17272.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143292 restraints weight = 9290.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147062 restraints weight = 6171.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149633 restraints weight = 4669.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151426 restraints weight = 3857.168| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11830 Z= 0.110 Angle : 0.569 9.763 16016 Z= 0.280 Chirality : 0.040 0.158 1884 Planarity : 0.004 0.051 1992 Dihedral : 7.718 72.215 1644 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.47 % Allowed : 30.51 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.22), residues: 1446 helix: 0.31 (0.18), residues: 804 sheet: 0.47 (0.44), residues: 130 loop : -1.42 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.011 0.001 TYR B 113 PHE 0.008 0.001 PHE A 432 TRP 0.011 0.001 TRP A 411 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00249 (11830) covalent geometry : angle 0.56933 (16016) hydrogen bonds : bond 0.03360 ( 556) hydrogen bonds : angle 4.48738 ( 1596) *********************** 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 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8199 (m-80) cc_final: 0.7940 (m-80) REVERT: A 300 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7882 (t0) REVERT: A 344 CYS cc_start: 0.8390 (m) cc_final: 0.8152 (p) REVERT: A 361 PHE cc_start: 0.5187 (OUTLIER) cc_final: 0.4000 (t80) REVERT: A 550 MET cc_start: 0.6334 (tmm) cc_final: 0.5760 (tmm) REVERT: A 587 MET cc_start: 0.8047 (tpt) cc_final: 0.7616 (tmm) REVERT: A 639 MET cc_start: 0.4547 (mmp) cc_final: 0.4243 (mmp) REVERT: A 741 TYR cc_start: 0.7545 (m-80) cc_final: 0.6664 (m-80) REVERT: A 775 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6748 (tt0) REVERT: A 888 GLN cc_start: 0.7853 (tp40) cc_final: 0.7445 (tt0) REVERT: B 110 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7681 (p0) REVERT: B 146 PHE cc_start: 0.8231 (m-80) cc_final: 0.7966 (m-80) REVERT: B 152 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (tp30) REVERT: B 300 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 344 CYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8401 (p) REVERT: B 361 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4059 (t80) REVERT: B 550 MET cc_start: 0.6379 (tmm) cc_final: 0.5771 (tmm) REVERT: B 639 MET cc_start: 0.4508 (mmp) cc_final: 0.4214 (mmp) REVERT: B 741 TYR cc_start: 0.7477 (m-80) cc_final: 0.6630 (m-80) REVERT: B 775 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6842 (tt0) REVERT: B 888 GLN cc_start: 0.7833 (tp40) cc_final: 0.7368 (tt0) outliers start: 56 outliers final: 36 residues processed: 220 average time/residue: 0.0880 time to fit residues: 29.6655 Evaluate side-chains 203 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU 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 662 THR 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 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 344 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE 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 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 722 SER 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 78 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 76 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.175078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141617 restraints weight = 17105.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146841 restraints weight = 9154.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150549 restraints weight = 6070.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153023 restraints weight = 4577.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154759 restraints weight = 3772.965| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2483 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= 0.115 Angle : 0.572 9.438 16016 Z= 0.282 Chirality : 0.040 0.150 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.541 71.641 1644 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.33 % Rotamer: Outliers : 4.15 % Allowed : 30.99 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1446 helix: 0.48 (0.18), residues: 798 sheet: 0.51 (0.44), residues: 130 loop : -1.35 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.012 0.001 TYR A 171 PHE 0.009 0.001 PHE B 670 TRP 0.013 0.001 TRP A 411 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00266 (11830) covalent geometry : angle 0.57229 (16016) hydrogen bonds : bond 0.03169 ( 556) hydrogen bonds : angle 4.37177 ( 1596) *********************** 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 227 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8194 (m-80) cc_final: 0.7925 (m-80) REVERT: A 300 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 344 CYS cc_start: 0.8446 (m) cc_final: 0.8159 (p) REVERT: A 550 MET cc_start: 0.6322 (tmm) cc_final: 0.5741 (tmm) REVERT: A 587 MET cc_start: 0.8002 (tpt) cc_final: 0.7584 (tmm) REVERT: A 674 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 680 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: A 741 TYR cc_start: 0.7027 (m-80) cc_final: 0.6705 (m-80) REVERT: A 775 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6643 (tt0) REVERT: A 888 GLN cc_start: 0.7823 (tp40) cc_final: 0.7431 (tt0) REVERT: B 146 PHE cc_start: 0.8243 (m-80) cc_final: 0.7964 (m-80) REVERT: B 152 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: B 300 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7740 (t0) REVERT: B 344 CYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 550 MET cc_start: 0.6412 (tmm) cc_final: 0.5817 (tmm) REVERT: B 587 MET cc_start: 0.8010 (tpt) cc_final: 0.7607 (tmm) REVERT: B 680 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: B 741 TYR cc_start: 0.6928 (m-80) cc_final: 0.6632 (m-80) REVERT: B 775 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6630 (tt0) REVERT: B 888 GLN cc_start: 0.7824 (tp40) cc_final: 0.7398 (tt0) outliers start: 52 outliers final: 37 residues processed: 210 average time/residue: 0.0838 time to fit residues: 26.6657 Evaluate side-chains 199 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 344 CYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.172991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139654 restraints weight = 17159.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144811 restraints weight = 9208.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.148350 restraints weight = 6116.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150804 restraints weight = 4634.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152399 restraints weight = 3828.214| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2615 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= 0.141 Angle : 0.607 9.652 16016 Z= 0.294 Chirality : 0.041 0.148 1884 Planarity : 0.004 0.055 1992 Dihedral : 7.464 70.714 1644 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 4.39 % Allowed : 30.75 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1446 helix: 0.52 (0.19), residues: 798 sheet: 0.36 (0.44), residues: 130 loop : -1.30 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.010 0.001 TYR B 283 PHE 0.015 0.001 PHE B 432 TRP 0.013 0.001 TRP A 411 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00339 (11830) covalent geometry : angle 0.60661 (16016) hydrogen bonds : bond 0.03204 ( 556) hydrogen bonds : angle 4.39899 ( 1596) *********************** 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 223 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8617 (mt) cc_final: 0.8400 (mt) REVERT: A 146 PHE cc_start: 0.8211 (m-80) cc_final: 0.7952 (m-80) REVERT: A 344 CYS cc_start: 0.8482 (m) cc_final: 0.8182 (p) REVERT: A 361 PHE cc_start: 0.5174 (OUTLIER) cc_final: 0.4143 (t80) REVERT: A 550 MET cc_start: 0.6282 (tmm) cc_final: 0.5730 (tmm) REVERT: A 587 MET cc_start: 0.8003 (tpt) cc_final: 0.7620 (tmm) REVERT: A 680 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7299 (mpp) REVERT: A 729 ILE cc_start: 0.7985 (pt) cc_final: 0.7487 (mm) REVERT: A 741 TYR cc_start: 0.7153 (m-80) cc_final: 0.6661 (m-80) REVERT: A 775 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6750 (tt0) REVERT: A 815 PHE cc_start: 0.7951 (m-80) cc_final: 0.7649 (m-80) REVERT: A 888 GLN cc_start: 0.7817 (tp40) cc_final: 0.7416 (tt0) REVERT: B 92 MET cc_start: 0.7880 (tpp) cc_final: 0.7655 (tpp) REVERT: B 130 LEU cc_start: 0.8608 (mt) cc_final: 0.8398 (mt) REVERT: B 146 PHE cc_start: 0.8235 (m-80) cc_final: 0.7952 (m-80) REVERT: B 344 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 361 PHE cc_start: 0.5187 (OUTLIER) cc_final: 0.4141 (t80) REVERT: B 550 MET cc_start: 0.6281 (tmm) cc_final: 0.5709 (tmm) REVERT: B 587 MET cc_start: 0.8017 (tpt) cc_final: 0.7645 (tmm) REVERT: B 680 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: B 741 TYR cc_start: 0.7023 (m-80) cc_final: 0.6607 (m-80) REVERT: B 775 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6743 (tt0) REVERT: B 815 PHE cc_start: 0.7954 (m-80) cc_final: 0.7644 (m-80) REVERT: B 888 GLN cc_start: 0.7820 (tp40) cc_final: 0.7394 (tt0) outliers start: 55 outliers final: 41 residues processed: 206 average time/residue: 0.0781 time to fit residues: 25.1606 Evaluate side-chains 199 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 MET 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 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 631 ILE 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 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 339 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 MET 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 631 ILE 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 42 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 99 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.175785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142159 restraints weight = 16941.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147419 restraints weight = 9091.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151092 restraints weight = 6025.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153566 restraints weight = 4553.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155344 restraints weight = 3750.504| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2757 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= 0.110 Angle : 0.588 12.021 16016 Z= 0.284 Chirality : 0.040 0.149 1884 Planarity : 0.004 0.055 1992 Dihedral : 7.315 69.862 1644 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.61 % Rotamer: Outliers : 3.75 % Allowed : 31.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1446 helix: 0.58 (0.18), residues: 798 sheet: 0.36 (0.44), residues: 130 loop : -1.32 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.010 0.001 TYR B 113 PHE 0.018 0.001 PHE A 87 TRP 0.016 0.001 TRP B 411 HIS 0.003 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00256 (11830) covalent geometry : angle 0.58764 (16016) hydrogen bonds : bond 0.02987 ( 556) hydrogen bonds : angle 4.27992 ( 1596) *********************** 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 217 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 PHE cc_start: 0.8228 (m-80) cc_final: 0.7970 (m-80) REVERT: A 300 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7842 (t0) REVERT: A 344 CYS cc_start: 0.8475 (m) cc_final: 0.8174 (p) REVERT: A 440 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7008 (tp) REVERT: A 550 MET cc_start: 0.6401 (tmm) cc_final: 0.5840 (tmm) REVERT: A 587 MET cc_start: 0.7964 (tpt) cc_final: 0.7590 (tmm) REVERT: A 680 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: A 729 ILE cc_start: 0.7813 (pt) cc_final: 0.7437 (mm) REVERT: A 741 TYR cc_start: 0.6979 (m-80) cc_final: 0.6579 (m-80) REVERT: A 815 PHE cc_start: 0.7960 (m-80) cc_final: 0.7695 (m-80) REVERT: A 873 ARG cc_start: 0.8407 (ttp80) cc_final: 0.7681 (tpp80) REVERT: A 888 GLN cc_start: 0.7821 (tp40) cc_final: 0.7470 (tt0) REVERT: B 92 MET cc_start: 0.7849 (tpp) cc_final: 0.7609 (tpp) REVERT: B 130 LEU cc_start: 0.8601 (mt) cc_final: 0.8377 (mt) REVERT: B 146 PHE cc_start: 0.8254 (m-80) cc_final: 0.7991 (m-80) REVERT: B 300 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 344 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 361 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4190 (t80) REVERT: B 550 MET cc_start: 0.6398 (tmm) cc_final: 0.5832 (tmm) REVERT: B 587 MET cc_start: 0.8001 (tpt) cc_final: 0.7628 (tmm) REVERT: B 680 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7196 (mpp) REVERT: B 741 TYR cc_start: 0.6957 (m-80) cc_final: 0.6573 (m-80) REVERT: B 775 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6694 (tt0) REVERT: B 815 PHE cc_start: 0.7933 (m-80) cc_final: 0.7651 (m-80) REVERT: B 873 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7688 (tpp80) REVERT: B 888 GLN cc_start: 0.7804 (tp40) cc_final: 0.7439 (tt0) outliers start: 47 outliers final: 35 residues processed: 202 average time/residue: 0.0816 time to fit residues: 26.0541 Evaluate side-chains 194 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU 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 792 GLU Chi-restraints excluded: chain A residue 793 LEU 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 344 CYS Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE 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 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 793 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.173428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139561 restraints weight = 17120.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144789 restraints weight = 9257.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148375 restraints weight = 6166.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150835 restraints weight = 4686.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152524 restraints weight = 3860.383| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2859 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= 0.142 Angle : 0.622 11.745 16016 Z= 0.298 Chirality : 0.041 0.165 1884 Planarity : 0.004 0.054 1992 Dihedral : 7.265 68.640 1644 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 4.79 % Allowed : 30.99 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1446 helix: 0.51 (0.18), residues: 800 sheet: 0.35 (0.44), residues: 130 loop : -1.22 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.010 0.001 TYR B 283 PHE 0.009 0.001 PHE B 432 TRP 0.016 0.001 TRP A 411 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00342 (11830) covalent geometry : angle 0.62151 (16016) hydrogen bonds : bond 0.03081 ( 556) hydrogen bonds : angle 4.42581 ( 1596) *********************** 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 211 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8644 (mt) cc_final: 0.8393 (mt) REVERT: A 146 PHE cc_start: 0.8220 (m-80) cc_final: 0.7970 (m-80) REVERT: A 300 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 344 CYS cc_start: 0.8474 (m) cc_final: 0.8185 (p) REVERT: A 550 MET cc_start: 0.6350 (tmm) cc_final: 0.5797 (tmm) REVERT: A 587 MET cc_start: 0.7981 (tpt) cc_final: 0.7613 (tmm) REVERT: A 680 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7343 (mpp) REVERT: A 741 TYR cc_start: 0.7100 (m-80) cc_final: 0.6693 (m-80) REVERT: A 775 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6283 (tm-30) REVERT: A 815 PHE cc_start: 0.8005 (m-80) cc_final: 0.7726 (m-80) REVERT: A 888 GLN cc_start: 0.7825 (tp40) cc_final: 0.7462 (tt0) REVERT: B 92 MET cc_start: 0.7842 (tpp) cc_final: 0.7606 (tpp) REVERT: B 130 LEU cc_start: 0.8621 (mt) cc_final: 0.8376 (mt) REVERT: B 146 PHE cc_start: 0.8241 (m-80) cc_final: 0.7979 (m-80) REVERT: B 300 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 344 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8044 (p) REVERT: B 361 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4366 (t80) REVERT: B 550 MET cc_start: 0.6377 (tmm) cc_final: 0.5824 (tmm) REVERT: B 587 MET cc_start: 0.8014 (tpt) cc_final: 0.7650 (tmm) REVERT: B 680 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7374 (mpp) REVERT: B 741 TYR cc_start: 0.7013 (m-80) cc_final: 0.6642 (m-80) REVERT: B 815 PHE cc_start: 0.7981 (m-80) cc_final: 0.7688 (m-80) REVERT: B 888 GLN cc_start: 0.7821 (tp40) cc_final: 0.7441 (tt0) outliers start: 60 outliers final: 44 residues processed: 194 average time/residue: 0.0748 time to fit residues: 23.2257 Evaluate side-chains 198 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 ASN Chi-restraints excluded: chain A residue 329 LEU 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 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 631 ILE 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 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 344 CYS 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 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 631 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.172582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138915 restraints weight = 17017.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144051 restraints weight = 9239.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.147552 restraints weight = 6184.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149912 restraints weight = 4716.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151652 restraints weight = 3913.286| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2951 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= 0.152 Angle : 0.632 11.606 16016 Z= 0.305 Chirality : 0.041 0.156 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.203 67.074 1644 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.95 % Favored : 93.91 % Rotamer: Outliers : 4.55 % Allowed : 31.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1446 helix: 0.45 (0.18), residues: 798 sheet: 0.30 (0.44), residues: 130 loop : -1.23 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.045 0.002 TYR B 652 PHE 0.020 0.001 PHE A 87 TRP 0.013 0.001 TRP A 411 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00367 (11830) covalent geometry : angle 0.63174 (16016) hydrogen bonds : bond 0.03127 ( 556) hydrogen bonds : angle 4.47916 ( 1596) *********************** 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 207 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8636 (mt) cc_final: 0.8363 (mt) REVERT: A 146 PHE cc_start: 0.8247 (m-80) cc_final: 0.7989 (m-80) REVERT: A 300 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7779 (t0) REVERT: A 344 CYS cc_start: 0.8479 (m) cc_final: 0.8186 (p) REVERT: A 361 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.4424 (t80) REVERT: A 550 MET cc_start: 0.6395 (tmm) cc_final: 0.5848 (tmm) REVERT: A 587 MET cc_start: 0.7996 (tpt) cc_final: 0.7638 (tmm) REVERT: A 680 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7449 (mpp) REVERT: A 741 TYR cc_start: 0.7056 (m-80) cc_final: 0.6693 (m-80) REVERT: A 775 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6308 (tm-30) REVERT: A 815 PHE cc_start: 0.8040 (m-80) cc_final: 0.7741 (m-80) REVERT: A 873 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7652 (tpp80) REVERT: A 888 GLN cc_start: 0.7833 (tp40) cc_final: 0.7481 (tt0) REVERT: B 92 MET cc_start: 0.7838 (tpp) cc_final: 0.7633 (tpp) REVERT: B 130 LEU cc_start: 0.8639 (mt) cc_final: 0.8369 (mt) REVERT: B 146 PHE cc_start: 0.8268 (m-80) cc_final: 0.8008 (m-80) REVERT: B 152 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: B 300 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7757 (t0) REVERT: B 344 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8079 (p) REVERT: B 361 PHE cc_start: 0.5437 (OUTLIER) cc_final: 0.4549 (t80) REVERT: B 550 MET cc_start: 0.6389 (tmm) cc_final: 0.5828 (tmm) REVERT: B 587 MET cc_start: 0.8029 (tpt) cc_final: 0.7664 (tmm) REVERT: B 680 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: B 741 TYR cc_start: 0.7000 (m-80) cc_final: 0.6662 (m-80) REVERT: B 815 PHE cc_start: 0.8022 (m-80) cc_final: 0.7716 (m-80) REVERT: B 873 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7642 (tpp80) REVERT: B 888 GLN cc_start: 0.7875 (tp40) cc_final: 0.7504 (tt0) outliers start: 57 outliers final: 42 residues processed: 190 average time/residue: 0.0773 time to fit residues: 23.3729 Evaluate side-chains 195 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 ASN Chi-restraints excluded: chain A residue 329 LEU 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 631 ILE 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 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 300 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 344 CYS 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 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 631 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 110 optimal weight: 0.8980 chunk 130 optimal weight: 0.0970 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142049 restraints weight = 17016.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147336 restraints weight = 9121.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150954 restraints weight = 6046.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153431 restraints weight = 4578.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155229 restraints weight = 3780.845| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11830 Z= 0.114 Angle : 0.608 11.501 16016 Z= 0.294 Chirality : 0.040 0.150 1884 Planarity : 0.004 0.054 1992 Dihedral : 7.019 65.438 1644 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 3.67 % Allowed : 32.83 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.22), residues: 1446 helix: 0.54 (0.18), residues: 800 sheet: 0.45 (0.44), residues: 130 loop : -1.30 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 873 TYR 0.050 0.002 TYR A 652 PHE 0.025 0.001 PHE B 87 TRP 0.025 0.001 TRP B 411 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00267 (11830) covalent geometry : angle 0.60753 (16016) hydrogen bonds : bond 0.02911 ( 556) hydrogen bonds : angle 4.31778 ( 1596) ********************** 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: 46 poor density : 158 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8637 (mt) cc_final: 0.8366 (mt) REVERT: A 146 PHE cc_start: 0.8237 (m-80) cc_final: 0.7984 (m-80) REVERT: A 300 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7863 (t0) REVERT: A 344 CYS cc_start: 0.8465 (m) cc_final: 0.8165 (p) REVERT: A 440 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7014 (tp) REVERT: A 550 MET cc_start: 0.6407 (tmm) cc_final: 0.5846 (tmm) REVERT: A 587 MET cc_start: 0.7991 (tpt) cc_final: 0.7624 (tmm) REVERT: A 680 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7204 (mpp) REVERT: A 741 TYR cc_start: 0.6870 (m-80) cc_final: 0.6480 (m-80) REVERT: A 775 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6275 (tm-30) REVERT: A 815 PHE cc_start: 0.8035 (m-80) cc_final: 0.7741 (m-80) REVERT: A 873 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7756 (tpp80) REVERT: A 888 GLN cc_start: 0.7862 (tp40) cc_final: 0.7515 (tt0) REVERT: B 92 MET cc_start: 0.7820 (tpp) cc_final: 0.7610 (tpp) REVERT: B 130 LEU cc_start: 0.8637 (mt) cc_final: 0.8376 (mt) REVERT: B 146 PHE cc_start: 0.8243 (m-80) cc_final: 0.7990 (m-80) REVERT: B 300 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.7812 (t0) REVERT: B 344 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 550 MET cc_start: 0.6397 (tmm) cc_final: 0.5842 (tmm) REVERT: B 587 MET cc_start: 0.8000 (tpt) cc_final: 0.7617 (tmm) REVERT: B 680 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: B 741 TYR cc_start: 0.6778 (m-80) cc_final: 0.6426 (m-80) REVERT: B 815 PHE cc_start: 0.7988 (m-80) cc_final: 0.7677 (m-80) REVERT: B 873 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7671 (tpp80) outliers start: 46 outliers final: 39 residues processed: 187 average time/residue: 0.0781 time to fit residues: 23.3823 Evaluate side-chains 192 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 ASN Chi-restraints excluded: chain A residue 329 LEU 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 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 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 344 CYS 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 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140082 restraints weight = 17049.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145282 restraints weight = 9190.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148844 restraints weight = 6114.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151292 restraints weight = 4639.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.153011 restraints weight = 3839.099| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3099 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= 0.141 Angle : 0.630 11.330 16016 Z= 0.304 Chirality : 0.041 0.151 1884 Planarity : 0.004 0.053 1992 Dihedral : 6.925 63.552 1644 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 3.67 % Allowed : 32.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1446 helix: 0.55 (0.18), residues: 798 sheet: 0.42 (0.45), residues: 128 loop : -1.25 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 873 TYR 0.039 0.002 TYR A 652 PHE 0.009 0.001 PHE B 432 TRP 0.017 0.001 TRP B 411 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00340 (11830) covalent geometry : angle 0.62998 (16016) hydrogen bonds : bond 0.02989 ( 556) hydrogen bonds : angle 4.41711 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.29 seconds wall clock time: 34 minutes 2.52 seconds (2042.52 seconds total)