Starting phenix.real_space_refine on Sat Sep 12 07:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.map" model { file = "/net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltt_63380/09_2026/9ltt_63380.cif" } resolution = 3.84 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= 0.010 sd= 0.090 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 77 5.49 5 S 40 5.16 5 C 9087 2.51 5 N 2401 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14349 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6320 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 35, 'TRANS': 794} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6251 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 34, 'TRANS': 786} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 60} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'PGW': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'PGW': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 3.69, per 1000 atoms: 0.26 Number of scatterers: 14349 At special positions: 0 Unit cell: (139.076, 122.067, 121.066, 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 40 16.00 P 77 15.00 O 2744 8.00 N 2401 7.00 C 9087 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 622.0 milliseconds 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 71.1% alpha, 10.1% beta 21 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.519A pdb=" N THR A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 94 removed outlier: 3.947A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.690A pdb=" N THR A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 138 through 168 Processing helix chain 'A' and resid 168 through 177 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 179 through 201 Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.749A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.698A pdb=" N HIS A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.221A pdb=" N LEU A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 361 removed outlier: 3.907A pdb=" N ARG A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.736A pdb=" N TYR A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 405 removed outlier: 3.520A pdb=" N SER A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.682A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 464 through 486 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.539A pdb=" N ARG A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 removed outlier: 3.960A pdb=" N LYS A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 599 through 614 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 680 through 686 Proline residue: A 685 - end of helix Processing helix chain 'A' and resid 687 through 702 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 762 through 778 Processing helix chain 'A' and resid 805 through 818 removed outlier: 3.781A pdb=" N ASN A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.520A pdb=" N LYS A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 859 removed outlier: 4.017A pdb=" N ALA A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 49 Processing helix chain 'B' and resid 53 through 64 removed outlier: 3.509A pdb=" N THR B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 94 removed outlier: 3.957A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.690A pdb=" N THR B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 removed outlier: 3.507A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 168 Processing helix chain 'B' and resid 168 through 177 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 179 through 201 Processing helix chain 'B' and resid 218 through 244 removed outlier: 3.733A pdb=" N LEU B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.694A pdb=" N HIS B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 306 through 322 removed outlier: 4.204A pdb=" N LEU B 310 " --> pdb=" O HIS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 361 removed outlier: 3.851A pdb=" N ARG B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.735A pdb=" N TYR B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 405 removed outlier: 3.971A pdb=" N ARG B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 430 removed outlier: 3.671A pdb=" N LEU B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 464 through 486 Processing helix chain 'B' and resid 492 through 498 Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.529A pdb=" N ARG B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 552 removed outlier: 3.959A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 599 through 614 Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 680 through 686 Proline residue: B 685 - end of helix Processing helix chain 'B' and resid 687 through 702 Processing helix chain 'B' and resid 715 through 720 Processing helix chain 'B' and resid 762 through 778 Processing helix chain 'B' and resid 805 through 818 removed outlier: 3.504A pdb=" N PHE B 816 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 828 removed outlier: 3.519A pdb=" N LYS B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 859 removed outlier: 3.996A pdb=" N ALA B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 570 removed outlier: 7.213A pdb=" N PHE A 577 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP A 592 " --> pdb=" O PHE A 577 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N MET A 579 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 623 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR A 837 " --> pdb=" O GLN A 622 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 838 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS A 640 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 840 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA A 638 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU A 643 " --> pdb=" O MET A 787 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET A 787 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA A 645 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 748 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A 786 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N ILE A 750 " --> pdb=" O GLY A 786 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ALA A 788 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 17.064A pdb=" N LEU A 752 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN A 738 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 753 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 736 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 755 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL A 734 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 729 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA4, first strand: chain 'B' and resid 567 through 570 removed outlier: 7.254A pdb=" N PHE B 577 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP B 592 " --> pdb=" O PHE B 577 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET B 579 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE B 623 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR B 837 " --> pdb=" O GLN B 622 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 838 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS B 640 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 840 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA B 638 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU B 643 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET B 787 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA B 645 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 748 " --> pdb=" O ASN B 784 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY B 786 " --> pdb=" O GLY B 748 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N ILE B 750 " --> pdb=" O GLY B 786 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ALA B 788 " --> pdb=" O ILE B 750 " (cutoff:3.500A) removed outlier: 17.091A pdb=" N LEU B 752 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN B 738 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET B 753 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE B 736 " --> pdb=" O MET B 753 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE B 755 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL B 734 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS B 729 " --> pdb=" O ILE B 733 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2628 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2153 1.32 - 1.45: 4236 1.45 - 1.57: 8192 1.57 - 1.69: 153 1.69 - 1.81: 74 Bond restraints: 14808 Sorted by residual: bond pdb=" C6 G C 19 " pdb=" N1 G C 19 " ideal model delta sigma weight residual 1.391 1.413 -0.022 7.00e-03 2.04e+04 9.63e+00 bond pdb=" C LEU B 244 " pdb=" N PRO B 245 " ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 8.97e+00 bond pdb=" N3 G C 19 " pdb=" C4 G C 19 " ideal model delta sigma weight residual 1.350 1.371 -0.021 7.00e-03 2.04e+04 8.90e+00 bond pdb=" N7 G C 19 " pdb=" C5 G C 19 " ideal model delta sigma weight residual 1.388 1.405 -0.017 6.00e-03 2.78e+04 8.43e+00 bond pdb=" P G C 1 " pdb=" OP2 G C 1 " ideal model delta sigma weight residual 1.485 1.543 -0.058 2.00e-02 2.50e+03 8.34e+00 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 19309 2.63 - 5.27: 1051 5.27 - 7.90: 56 7.90 - 10.54: 11 10.54 - 13.17: 3 Bond angle restraints: 20430 Sorted by residual: angle pdb=" N VAL A 473 " pdb=" CA VAL A 473 " pdb=" CB VAL A 473 " ideal model delta sigma weight residual 110.58 120.62 -10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" N VAL B 473 " pdb=" CA VAL B 473 " pdb=" CB VAL B 473 " ideal model delta sigma weight residual 110.58 120.56 -9.98 1.50e+00 4.44e-01 4.43e+01 angle pdb=" N VAL B 397 " pdb=" CA VAL B 397 " pdb=" CB VAL B 397 " ideal model delta sigma weight residual 110.58 119.50 -8.92 1.50e+00 4.44e-01 3.53e+01 angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" CB VAL A 397 " ideal model delta sigma weight residual 110.58 119.45 -8.87 1.50e+00 4.44e-01 3.50e+01 angle pdb=" CA PHE B 254 " pdb=" CB PHE B 254 " pdb=" CG PHE B 254 " ideal model delta sigma weight residual 113.80 108.05 5.75 1.00e+00 1.00e+00 3.31e+01 ... (remaining 20425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 8356 30.18 - 60.36: 370 60.36 - 90.54: 118 90.54 - 120.72: 19 120.72 - 150.90: 9 Dihedral angle restraints: 8872 sinusoidal: 4158 harmonic: 4714 Sorted by residual: dihedral pdb=" CA PHE A 119 " pdb=" C PHE A 119 " pdb=" N GLY A 120 " pdb=" CA GLY A 120 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE B 119 " pdb=" C PHE B 119 " pdb=" N GLY B 120 " pdb=" CA GLY B 120 " ideal model delta harmonic sigma weight residual -180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C5' G C 18 " pdb=" C4' G C 18 " pdb=" C3' G C 18 " pdb=" O3' G C 18 " ideal model delta sinusoidal sigma weight residual 147.00 114.34 32.66 1 8.00e+00 1.56e-02 2.37e+01 ... (remaining 8869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2259 0.135 - 0.270: 168 0.270 - 0.404: 2 0.404 - 0.539: 0 0.539 - 0.674: 1 Chirality restraints: 2430 Sorted by residual: chirality pdb=" P G C 1 " pdb=" OP1 G C 1 " pdb=" OP2 G C 1 " pdb=" O5' G C 1 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA GLN B 553 " pdb=" N GLN B 553 " pdb=" C GLN B 553 " pdb=" CB GLN B 553 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2427 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -0.277 9.50e-02 1.11e+02 1.24e-01 1.02e+01 pdb=" NE ARG A 128 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 449 " -0.270 9.50e-02 1.11e+02 1.22e-01 1.00e+01 pdb=" NE ARG A 449 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 449 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 449 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 449 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 454 " -0.230 9.50e-02 1.11e+02 1.03e-01 7.20e+00 pdb=" NE ARG B 454 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 454 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 454 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 454 " -0.013 2.00e-02 2.50e+03 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 5427 2.92 - 3.42: 14573 3.42 - 3.91: 24960 3.91 - 4.41: 28065 4.41 - 4.90: 44867 Nonbonded interactions: 117892 Sorted by model distance: nonbonded pdb=" O ALA B 234 " pdb=" OG SER B 238 " model vdw 2.426 3.040 nonbonded pdb=" O ALA A 234 " pdb=" OG SER A 238 " model vdw 2.452 3.040 nonbonded pdb=" N THR A 365 " pdb=" OE2 GLU A 504 " model vdw 2.459 3.120 nonbonded pdb=" O VAL B 358 " pdb=" OG SER B 361 " model vdw 2.463 3.040 nonbonded pdb=" N THR B 365 " pdb=" OE2 GLU B 504 " model vdw 2.466 3.120 ... (remaining 117887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 530 or resid 534 through 791 or resid 804 throu \ gh 903)) 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.008 0.058 14810 Z= 0.532 Angle : 1.329 13.169 20430 Z= 0.878 Chirality : 0.072 0.674 2430 Planarity : 0.010 0.124 2285 Dihedral : 19.394 150.898 5842 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.20 % Favored : 97.62 % Rotamer: Outliers : 2.33 % Allowed : 6.74 % Favored : 90.93 % Cbeta Deviations : 0.13 % 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 are not related in a simple way. whole: 1.58 (0.20), residues: 1637 helix: 1.72 (0.15), residues: 1090 sheet: 1.32 (0.43), residues: 126 loop : -0.80 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG A 449 TYR 0.027 0.004 TYR A 129 PHE 0.035 0.003 PHE B 254 TRP 0.033 0.003 TRP B 222 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.53 (14808) covalent geometry : angle 1.32911 / 0.88 (20430) hydrogen bonds : bond 0.16144 / 10.88 ( 973) hydrogen bonds : angle 5.98002 / 4.45 ( 2734) Misc. bond : bond 0.04672 / 2.35 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LEU cc_start: 0.8510 (tp) cc_final: 0.8247 (tt) REVERT: A 214 ILE cc_start: 0.8455 (mt) cc_final: 0.8033 (tt) REVERT: A 241 TYR cc_start: 0.8728 (t80) cc_final: 0.8370 (t80) REVERT: A 278 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 377 LEU cc_start: 0.8571 (mp) cc_final: 0.8318 (mp) REVERT: A 512 LEU cc_start: 0.7802 (tp) cc_final: 0.7448 (tt) REVERT: A 722 GLN cc_start: 0.8737 (mt0) cc_final: 0.8531 (mt0) REVERT: A 736 PHE cc_start: 0.7294 (p90) cc_final: 0.6629 (p90) REVERT: A 780 PHE cc_start: 0.8243 (m-80) cc_final: 0.7843 (m-10) REVERT: A 787 MET cc_start: 0.6562 (mmm) cc_final: 0.6267 (mmm) REVERT: A 802 TRP cc_start: 0.8090 (t60) cc_final: 0.7871 (t60) REVERT: A 825 PHE cc_start: 0.7423 (t80) cc_final: 0.7173 (t80) REVERT: A 847 MET cc_start: 0.7145 (mpm) cc_final: 0.6498 (ttm) REVERT: A 848 ILE cc_start: 0.7983 (mm) cc_final: 0.7429 (tt) REVERT: A 852 ASP cc_start: 0.7624 (m-30) cc_final: 0.7391 (m-30) REVERT: B 365 THR cc_start: 0.8973 (m) cc_final: 0.8670 (p) REVERT: B 370 LEU cc_start: 0.9092 (mt) cc_final: 0.8703 (mt) REVERT: B 536 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7042 (tm-30) REVERT: B 551 ARG cc_start: 0.9430 (mtm-85) cc_final: 0.9181 (mmm160) REVERT: B 579 MET cc_start: 0.7907 (ptt) cc_final: 0.7284 (ptp) REVERT: B 648 ASP cc_start: 0.8817 (t0) cc_final: 0.8364 (t0) REVERT: B 671 ARG cc_start: 0.8510 (mpp-170) cc_final: 0.8256 (mtt180) REVERT: B 703 ASN cc_start: 0.9386 (t0) cc_final: 0.9155 (p0) REVERT: B 757 PRO cc_start: 0.7208 (Cg_exo) cc_final: 0.6951 (Cg_endo) REVERT: B 811 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9362 (mm-30) REVERT: B 830 HIS cc_start: 0.8948 (m-70) cc_final: 0.8671 (m-70) REVERT: B 851 MET cc_start: 0.9540 (mmm) cc_final: 0.9207 (ttp) outliers start: 30 outliers final: 11 residues processed: 375 average time/residue: 0.1362 time to fit residues: 71.8698 Evaluate side-chains 206 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 449 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN B 225 GLN B 460 ASN B 702 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.172046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111451 restraints weight = 23925.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111627 restraints weight = 13026.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113005 restraints weight = 9282.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113459 restraints weight = 7630.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113539 restraints weight = 7577.327| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14810 Z= 0.183 Angle : 0.683 13.170 20430 Z= 0.358 Chirality : 0.042 0.143 2430 Planarity : 0.005 0.047 2285 Dihedral : 19.932 147.379 3129 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.80 % Rotamer: Outliers : 3.57 % Allowed : 13.49 % Favored : 82.95 % 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 are not related in a simple way. whole: 2.38 (0.20), residues: 1637 helix: 2.41 (0.15), residues: 1083 sheet: 1.02 (0.43), residues: 130 loop : -0.47 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 582 TYR 0.026 0.002 TYR B 817 PHE 0.025 0.002 PHE B 709 TRP 0.015 0.002 TRP B 222 HIS 0.011 0.001 HIS B 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (14808) covalent geometry : angle 0.68301 / 0.36 (20430) hydrogen bonds : bond 0.05941 / 4.04 ( 973) hydrogen bonds : angle 4.60629 / 3.43 ( 2734) Misc. bond : bond 0.00259 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8743 (mt) cc_final: 0.8489 (tt) REVERT: A 241 TYR cc_start: 0.8685 (t80) cc_final: 0.8428 (t80) REVERT: A 512 LEU cc_start: 0.8158 (tp) cc_final: 0.7695 (tt) REVERT: A 563 MET cc_start: 0.7476 (ttp) cc_final: 0.7178 (ttp) REVERT: A 753 MET cc_start: 0.6256 (ppp) cc_final: 0.5865 (ppp) REVERT: A 787 MET cc_start: 0.7453 (mmm) cc_final: 0.7206 (mmm) REVERT: A 847 MET cc_start: 0.6948 (mpm) cc_final: 0.6413 (ttm) REVERT: A 852 ASP cc_start: 0.7830 (m-30) cc_final: 0.7582 (m-30) REVERT: B 46 MET cc_start: 0.7112 (ttp) cc_final: 0.6906 (ttp) REVERT: B 52 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 370 LEU cc_start: 0.9247 (mt) cc_final: 0.8791 (mt) REVERT: B 376 TYR cc_start: 0.7265 (m-10) cc_final: 0.7054 (m-10) REVERT: B 515 ILE cc_start: 0.8819 (pt) cc_final: 0.8582 (mm) REVERT: B 579 MET cc_start: 0.7913 (ptt) cc_final: 0.7697 (ptp) REVERT: B 580 TYR cc_start: 0.8629 (p90) cc_final: 0.8327 (p90) REVERT: B 607 PHE cc_start: 0.8480 (t80) cc_final: 0.8116 (t80) REVERT: B 648 ASP cc_start: 0.8150 (t0) cc_final: 0.7852 (t0) REVERT: B 706 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6268 (tp30) REVERT: B 757 PRO cc_start: 0.7141 (Cg_exo) cc_final: 0.6913 (Cg_endo) REVERT: B 820 LYS cc_start: 0.8816 (pttt) cc_final: 0.8458 (pttt) REVERT: B 830 HIS cc_start: 0.8669 (m-70) cc_final: 0.8418 (m90) REVERT: B 832 HIS cc_start: 0.7568 (t-170) cc_final: 0.7324 (t-170) outliers start: 46 outliers final: 24 residues processed: 236 average time/residue: 0.1110 time to fit residues: 38.8848 Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 706 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.171348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110978 restraints weight = 24241.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111048 restraints weight = 13400.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111524 restraints weight = 11033.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111900 restraints weight = 9543.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112186 restraints weight = 8762.985| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14810 Z= 0.148 Angle : 0.604 11.585 20430 Z= 0.315 Chirality : 0.040 0.276 2430 Planarity : 0.005 0.059 2285 Dihedral : 19.327 143.397 3110 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 3.41 % Allowed : 15.58 % Favored : 81.01 % 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 are not related in a simple way. whole: 2.47 (0.21), residues: 1637 helix: 2.49 (0.15), residues: 1084 sheet: 0.91 (0.44), residues: 123 loop : -0.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 606 TYR 0.042 0.002 TYR B 817 PHE 0.028 0.002 PHE A 254 TRP 0.023 0.001 TRP A 497 HIS 0.005 0.001 HIS B 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (14808) covalent geometry : angle 0.60383 / 0.32 (20430) hydrogen bonds : bond 0.05144 / 3.50 ( 973) hydrogen bonds : angle 4.29559 / 3.20 ( 2734) Misc. bond : bond 0.00159 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.7179 (mp0) cc_final: 0.6919 (mp0) REVERT: A 512 LEU cc_start: 0.8197 (tp) cc_final: 0.7659 (tt) REVERT: A 563 MET cc_start: 0.7481 (ttp) cc_final: 0.7182 (ttp) REVERT: A 727 LEU cc_start: 0.8386 (mp) cc_final: 0.7795 (tp) REVERT: A 753 MET cc_start: 0.6258 (ppp) cc_final: 0.5771 (ppp) REVERT: A 787 MET cc_start: 0.7474 (mmm) cc_final: 0.7215 (mmm) REVERT: A 852 ASP cc_start: 0.7872 (m-30) cc_final: 0.7592 (m-30) REVERT: B 52 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 370 LEU cc_start: 0.9182 (mt) cc_final: 0.8896 (mt) REVERT: B 376 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: B 580 TYR cc_start: 0.8661 (p90) cc_final: 0.8281 (p90) REVERT: B 607 PHE cc_start: 0.8477 (t80) cc_final: 0.7874 (t80) REVERT: B 648 ASP cc_start: 0.8062 (t0) cc_final: 0.7673 (t0) REVERT: B 706 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6437 (tp30) REVERT: B 772 MET cc_start: 0.9151 (mpp) cc_final: 0.8902 (mmp) REVERT: B 815 ARG cc_start: 0.8799 (ttt180) cc_final: 0.8324 (ttt180) REVERT: B 830 HIS cc_start: 0.8690 (m-70) cc_final: 0.8419 (m90) REVERT: B 832 HIS cc_start: 0.7882 (t-170) cc_final: 0.7621 (t-170) outliers start: 44 outliers final: 33 residues processed: 196 average time/residue: 0.1092 time to fit residues: 32.0767 Evaluate side-chains 185 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 851 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 164 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 834 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.164793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105397 restraints weight = 24584.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103745 restraints weight = 14624.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104610 restraints weight = 12861.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104991 restraints weight = 10525.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105184 restraints weight = 9827.139| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14810 Z= 0.236 Angle : 0.699 10.935 20430 Z= 0.359 Chirality : 0.042 0.241 2430 Planarity : 0.006 0.085 2285 Dihedral : 18.929 143.897 3110 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.81 % Favored : 97.01 % Rotamer: Outliers : 5.43 % Allowed : 15.74 % Favored : 78.84 % 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 are not related in a simple way. whole: 2.09 (0.21), residues: 1637 helix: 2.13 (0.15), residues: 1088 sheet: 0.98 (0.45), residues: 131 loop : -0.48 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 606 TYR 0.052 0.002 TYR B 817 PHE 0.023 0.002 PHE A 38 TRP 0.031 0.002 TRP A 497 HIS 0.005 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (14808) covalent geometry : angle 0.69886 / 0.36 (20430) hydrogen bonds : bond 0.05387 / 3.64 ( 973) hydrogen bonds : angle 4.42455 / 3.31 ( 2734) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8666 (tp) cc_final: 0.8322 (tp) REVERT: A 356 MET cc_start: 0.8511 (ttp) cc_final: 0.8076 (ttt) REVERT: A 512 LEU cc_start: 0.8279 (tp) cc_final: 0.7752 (tt) REVERT: A 563 MET cc_start: 0.7682 (ttp) cc_final: 0.7395 (ttm) REVERT: A 727 LEU cc_start: 0.8247 (mp) cc_final: 0.7822 (tp) REVERT: A 753 MET cc_start: 0.6224 (ppp) cc_final: 0.5776 (ppp) REVERT: A 772 MET cc_start: 0.8206 (mtt) cc_final: 0.7970 (mmt) REVERT: A 852 ASP cc_start: 0.7790 (m-30) cc_final: 0.7580 (m-30) REVERT: B 370 LEU cc_start: 0.9185 (mt) cc_final: 0.8874 (mt) REVERT: B 376 TYR cc_start: 0.7416 (m-10) cc_final: 0.7200 (m-10) REVERT: B 580 TYR cc_start: 0.8630 (p90) cc_final: 0.8313 (p90) REVERT: B 603 LEU cc_start: 0.8763 (mt) cc_final: 0.8478 (mt) REVERT: B 605 TRP cc_start: 0.8665 (m100) cc_final: 0.8012 (m100) REVERT: B 607 PHE cc_start: 0.8517 (t80) cc_final: 0.7864 (t80) REVERT: B 648 ASP cc_start: 0.8005 (t0) cc_final: 0.7588 (t0) REVERT: B 654 MET cc_start: 0.6976 (tpp) cc_final: 0.6740 (tpp) REVERT: B 706 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6414 (tp30) REVERT: B 766 PHE cc_start: 0.8365 (t80) cc_final: 0.8108 (t80) REVERT: B 830 HIS cc_start: 0.8612 (m-70) cc_final: 0.8377 (m90) REVERT: B 832 HIS cc_start: 0.7983 (t-170) cc_final: 0.7656 (t-170) outliers start: 70 outliers final: 54 residues processed: 212 average time/residue: 0.1071 time to fit residues: 34.6289 Evaluate side-chains 194 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 851 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 6 optimal weight: 0.9990 chunk 145 optimal weight: 50.0000 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 166 optimal weight: 50.0000 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106553 restraints weight = 24530.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107203 restraints weight = 13813.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107728 restraints weight = 10153.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108097 restraints weight = 9256.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108254 restraints weight = 8489.212| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14810 Z= 0.134 Angle : 0.592 9.955 20430 Z= 0.304 Chirality : 0.039 0.287 2430 Planarity : 0.005 0.079 2285 Dihedral : 18.564 145.968 3110 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.75 % Favored : 97.13 % Rotamer: Outliers : 4.03 % Allowed : 17.98 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.21), residues: 1637 helix: 2.21 (0.15), residues: 1093 sheet: 1.65 (0.49), residues: 108 loop : -0.51 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 551 TYR 0.038 0.002 TYR B 817 PHE 0.025 0.002 PHE B 825 TRP 0.024 0.001 TRP A 222 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14808) covalent geometry : angle 0.59192 / 0.30 (20430) hydrogen bonds : bond 0.04688 / 3.17 ( 973) hydrogen bonds : angle 4.14537 / 3.10 ( 2734) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8976 (m-40) cc_final: 0.8765 (m110) REVERT: A 105 LEU cc_start: 0.8582 (tp) cc_final: 0.8269 (tp) REVERT: A 512 LEU cc_start: 0.8194 (tp) cc_final: 0.7645 (tt) REVERT: A 727 LEU cc_start: 0.8154 (mp) cc_final: 0.7551 (tp) REVERT: A 753 MET cc_start: 0.6313 (ppp) cc_final: 0.5834 (ppp) REVERT: B 83 LEU cc_start: 0.9338 (mt) cc_final: 0.9134 (tp) REVERT: B 105 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8627 (tt) REVERT: B 370 LEU cc_start: 0.9083 (mt) cc_final: 0.8789 (mt) REVERT: B 515 ILE cc_start: 0.8773 (pp) cc_final: 0.8351 (mm) REVERT: B 534 ARG cc_start: 0.6179 (mmm-85) cc_final: 0.5766 (mmt-90) REVERT: B 579 MET cc_start: 0.8042 (ttp) cc_final: 0.7686 (tpp) REVERT: B 580 TYR cc_start: 0.8675 (p90) cc_final: 0.8214 (p90) REVERT: B 603 LEU cc_start: 0.8910 (mt) cc_final: 0.8701 (mt) REVERT: B 605 TRP cc_start: 0.8665 (m100) cc_final: 0.7881 (m100) REVERT: B 607 PHE cc_start: 0.8390 (t80) cc_final: 0.7724 (t80) REVERT: B 648 ASP cc_start: 0.8046 (t0) cc_final: 0.7689 (t0) REVERT: B 671 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8197 (mtm180) REVERT: B 706 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6474 (tp30) REVERT: B 830 HIS cc_start: 0.8623 (m-70) cc_final: 0.8364 (m90) REVERT: B 832 HIS cc_start: 0.8134 (t-170) cc_final: 0.7765 (t-170) REVERT: B 855 PHE cc_start: 0.9123 (m-80) cc_final: 0.8912 (m-80) outliers start: 52 outliers final: 38 residues processed: 192 average time/residue: 0.1059 time to fit residues: 31.0000 Evaluate side-chains 186 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 155 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 169 optimal weight: 50.0000 chunk 22 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 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 = 0.4195 r_free = 0.4195 target = 0.164149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104368 restraints weight = 24469.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103748 restraints weight = 15107.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104410 restraints weight = 11810.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104898 restraints weight = 9750.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105024 restraints weight = 9135.194| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14810 Z= 0.176 Angle : 0.619 9.125 20430 Z= 0.312 Chirality : 0.039 0.179 2430 Planarity : 0.005 0.062 2285 Dihedral : 18.360 147.297 3110 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 4.34 % Allowed : 18.84 % Favored : 76.82 % 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 are not related in a simple way. whole: 2.23 (0.21), residues: 1637 helix: 2.20 (0.15), residues: 1093 sheet: 1.56 (0.49), residues: 114 loop : -0.44 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 606 TYR 0.032 0.002 TYR B 817 PHE 0.017 0.002 PHE A 38 TRP 0.021 0.002 TRP B 222 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (14808) covalent geometry : angle 0.61930 / 0.31 (20430) hydrogen bonds : bond 0.04770 / 3.22 ( 973) hydrogen bonds : angle 4.15996 / 3.11 ( 2734) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8985 (m-40) cc_final: 0.8677 (m-40) REVERT: A 105 LEU cc_start: 0.8657 (tp) cc_final: 0.8354 (tp) REVERT: A 512 LEU cc_start: 0.8226 (tp) cc_final: 0.7660 (tt) REVERT: A 727 LEU cc_start: 0.8123 (mp) cc_final: 0.7627 (tp) REVERT: A 753 MET cc_start: 0.6328 (ppp) cc_final: 0.5842 (ppp) REVERT: B 105 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8682 (tt) REVERT: B 249 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 427 LEU cc_start: 0.8207 (tt) cc_final: 0.7979 (tt) REVERT: B 515 ILE cc_start: 0.8835 (pp) cc_final: 0.8359 (mm) REVERT: B 579 MET cc_start: 0.8136 (ttp) cc_final: 0.7733 (tpp) REVERT: B 587 TRP cc_start: 0.8242 (m-10) cc_final: 0.7784 (m-10) REVERT: B 603 LEU cc_start: 0.8934 (mt) cc_final: 0.8594 (mt) REVERT: B 605 TRP cc_start: 0.8660 (m100) cc_final: 0.7847 (m100) REVERT: B 607 PHE cc_start: 0.8364 (t80) cc_final: 0.7726 (t80) REVERT: B 648 ASP cc_start: 0.8065 (t0) cc_final: 0.7687 (t0) REVERT: B 706 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6385 (tp30) REVERT: B 830 HIS cc_start: 0.8552 (m-70) cc_final: 0.8330 (m90) REVERT: B 832 HIS cc_start: 0.8150 (t-170) cc_final: 0.7711 (t-170) REVERT: B 837 TYR cc_start: 0.8404 (m-80) cc_final: 0.8173 (t80) outliers start: 56 outliers final: 48 residues processed: 190 average time/residue: 0.1080 time to fit residues: 31.4609 Evaluate side-chains 190 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 810 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 GLN B 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.168065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108818 restraints weight = 24218.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108416 restraints weight = 13572.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107943 restraints weight = 10920.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108748 restraints weight = 10170.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108979 restraints weight = 8678.666| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14810 Z= 0.119 Angle : 0.577 16.044 20430 Z= 0.289 Chirality : 0.038 0.180 2430 Planarity : 0.005 0.060 2285 Dihedral : 18.094 149.437 3110 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 3.33 % Allowed : 20.39 % Favored : 76.28 % 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 are not related in a simple way. whole: 2.46 (0.21), residues: 1637 helix: 2.41 (0.15), residues: 1076 sheet: 1.61 (0.49), residues: 110 loop : -0.32 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 582 TYR 0.033 0.002 TYR B 817 PHE 0.029 0.001 PHE B 766 TRP 0.026 0.001 TRP A 222 HIS 0.003 0.000 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (14808) covalent geometry : angle 0.57653 / 0.29 (20430) hydrogen bonds : bond 0.04194 / 2.83 ( 973) hydrogen bonds : angle 3.95351 / 2.94 ( 2734) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9481 (mt) cc_final: 0.9093 (tp) REVERT: A 105 LEU cc_start: 0.8595 (tp) cc_final: 0.8278 (tp) REVERT: A 310 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 376 TYR cc_start: 0.7227 (m-10) cc_final: 0.6954 (m-10) REVERT: A 499 PHE cc_start: 0.8065 (m-80) cc_final: 0.7835 (m-10) REVERT: A 512 LEU cc_start: 0.8114 (tp) cc_final: 0.7556 (tt) REVERT: A 578 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8771 (tt) REVERT: A 753 MET cc_start: 0.6219 (ppp) cc_final: 0.5768 (ppp) REVERT: B 83 LEU cc_start: 0.9325 (mt) cc_final: 0.9085 (tp) REVERT: B 105 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8641 (tt) REVERT: B 427 LEU cc_start: 0.8249 (tt) cc_final: 0.7704 (tt) REVERT: B 515 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 579 MET cc_start: 0.8078 (ttp) cc_final: 0.7718 (tpp) REVERT: B 580 TYR cc_start: 0.8540 (p90) cc_final: 0.8328 (p90) REVERT: B 587 TRP cc_start: 0.8246 (m-10) cc_final: 0.7677 (m-10) REVERT: B 603 LEU cc_start: 0.8931 (mt) cc_final: 0.8329 (mt) REVERT: B 605 TRP cc_start: 0.8785 (m100) cc_final: 0.7858 (m100) REVERT: B 607 PHE cc_start: 0.8551 (t80) cc_final: 0.7847 (t80) REVERT: B 648 ASP cc_start: 0.8085 (t0) cc_final: 0.7740 (t0) REVERT: B 706 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: B 830 HIS cc_start: 0.8650 (m-70) cc_final: 0.8367 (m90) REVERT: B 832 HIS cc_start: 0.8323 (t-170) cc_final: 0.7918 (t-170) outliers start: 43 outliers final: 28 residues processed: 191 average time/residue: 0.1144 time to fit residues: 32.7314 Evaluate side-chains 180 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 50.0000 chunk 122 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.180808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.127436 restraints weight = 24960.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128182 restraints weight = 18758.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128357 restraints weight = 16004.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.128894 restraints weight = 12157.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129225 restraints weight = 10374.382| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14810 Z= 0.165 Angle : 0.623 15.044 20430 Z= 0.309 Chirality : 0.039 0.180 2430 Planarity : 0.005 0.061 2285 Dihedral : 17.962 149.676 3109 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 3.64 % Allowed : 21.01 % Favored : 75.35 % 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 are not related in a simple way. whole: 2.36 (0.21), residues: 1637 helix: 2.33 (0.16), residues: 1083 sheet: 1.52 (0.49), residues: 110 loop : -0.38 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 401 TYR 0.034 0.002 TYR B 817 PHE 0.023 0.002 PHE B 766 TRP 0.022 0.001 TRP A 222 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (14808) covalent geometry : angle 0.62284 / 0.31 (20430) hydrogen bonds : bond 0.04452 / 3.02 ( 973) hydrogen bonds : angle 4.05537 / 3.02 ( 2734) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8709 (tp) cc_final: 0.8412 (tp) REVERT: A 310 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 461 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: A 512 LEU cc_start: 0.8242 (tp) cc_final: 0.7671 (tt) REVERT: A 753 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5643 (ppp) REVERT: A 772 MET cc_start: 0.8171 (mtt) cc_final: 0.7877 (mmt) REVERT: A 787 MET cc_start: 0.7511 (mmm) cc_final: 0.6986 (mtp) REVERT: B 105 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 373 LEU cc_start: 0.8735 (tp) cc_final: 0.8434 (pp) REVERT: B 515 ILE cc_start: 0.8933 (pp) cc_final: 0.8383 (mm) REVERT: B 587 TRP cc_start: 0.7860 (m-10) cc_final: 0.7574 (m-10) REVERT: B 603 LEU cc_start: 0.8703 (mt) cc_final: 0.8358 (mt) REVERT: B 605 TRP cc_start: 0.8118 (m100) cc_final: 0.7533 (m100) REVERT: B 607 PHE cc_start: 0.7798 (t80) cc_final: 0.7432 (t80) REVERT: B 648 ASP cc_start: 0.7674 (t0) cc_final: 0.7344 (t0) REVERT: B 832 HIS cc_start: 0.7669 (t-170) cc_final: 0.7266 (t-170) outliers start: 47 outliers final: 40 residues processed: 177 average time/residue: 0.1104 time to fit residues: 29.6304 Evaluate side-chains 180 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 105 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 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 = 0.4223 r_free = 0.4223 target = 0.167022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107836 restraints weight = 24780.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107178 restraints weight = 14661.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107580 restraints weight = 11466.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108069 restraints weight = 10191.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108442 restraints weight = 8999.521| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14810 Z= 0.119 Angle : 0.596 13.691 20430 Z= 0.296 Chirality : 0.038 0.187 2430 Planarity : 0.005 0.067 2285 Dihedral : 17.836 149.499 3109 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 3.26 % Allowed : 21.40 % Favored : 75.35 % 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 are not related in a simple way. whole: 2.43 (0.21), residues: 1637 helix: 2.42 (0.16), residues: 1076 sheet: 1.38 (0.49), residues: 110 loop : -0.35 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 401 TYR 0.034 0.002 TYR B 817 PHE 0.014 0.001 PHE B 277 TRP 0.025 0.001 TRP A 222 HIS 0.006 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14808) covalent geometry : angle 0.59575 / 0.30 (20430) hydrogen bonds : bond 0.04180 / 2.83 ( 973) hydrogen bonds : angle 3.94988 / 2.94 ( 2734) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9499 (mt) cc_final: 0.9147 (tp) REVERT: A 105 LEU cc_start: 0.8653 (tp) cc_final: 0.8354 (tp) REVERT: A 512 LEU cc_start: 0.8139 (tp) cc_final: 0.7567 (tt) REVERT: A 578 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 753 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5649 (ppp) REVERT: A 772 MET cc_start: 0.8219 (mtt) cc_final: 0.7857 (mmt) REVERT: A 787 MET cc_start: 0.7445 (mmm) cc_final: 0.6904 (mtp) REVERT: B 105 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8683 (tt) REVERT: B 373 LEU cc_start: 0.8679 (tp) cc_final: 0.8403 (pp) REVERT: B 515 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8281 (mm) REVERT: B 587 TRP cc_start: 0.8093 (m-10) cc_final: 0.7636 (m-10) REVERT: B 603 LEU cc_start: 0.8809 (mt) cc_final: 0.8463 (mt) REVERT: B 605 TRP cc_start: 0.8689 (m100) cc_final: 0.7815 (m100) REVERT: B 607 PHE cc_start: 0.8425 (t80) cc_final: 0.7763 (t80) REVERT: B 648 ASP cc_start: 0.8179 (t0) cc_final: 0.7812 (t0) REVERT: B 832 HIS cc_start: 0.8224 (t-170) cc_final: 0.7818 (t-170) outliers start: 42 outliers final: 35 residues processed: 169 average time/residue: 0.1124 time to fit residues: 29.0257 Evaluate side-chains 178 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 chunk 130 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 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 = 0.4237 r_free = 0.4237 target = 0.168400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108679 restraints weight = 24485.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109392 restraints weight = 13771.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108938 restraints weight = 10619.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109762 restraints weight = 10009.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109876 restraints weight = 8756.254| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14810 Z= 0.113 Angle : 0.592 12.607 20430 Z= 0.293 Chirality : 0.038 0.196 2430 Planarity : 0.004 0.067 2285 Dihedral : 17.564 151.145 3109 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.79 % Allowed : 22.02 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.21), residues: 1637 helix: 2.50 (0.16), residues: 1074 sheet: 1.17 (0.50), residues: 110 loop : -0.20 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 401 TYR 0.033 0.002 TYR B 817 PHE 0.018 0.001 PHE B 755 TRP 0.026 0.001 TRP A 222 HIS 0.003 0.000 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14808) covalent geometry : angle 0.59233 / 0.29 (20430) hydrogen bonds : bond 0.03875 / 2.63 ( 973) hydrogen bonds : angle 3.86104 / 2.87 ( 2734) Misc. bond : bond 0.00026 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8671 (m-80) cc_final: 0.8407 (m-10) REVERT: A 83 LEU cc_start: 0.9469 (mt) cc_final: 0.9178 (tp) REVERT: A 376 TYR cc_start: 0.7409 (m-10) cc_final: 0.7101 (m-10) REVERT: A 499 PHE cc_start: 0.8061 (m-80) cc_final: 0.7827 (m-10) REVERT: A 512 LEU cc_start: 0.8127 (tp) cc_final: 0.7603 (tt) REVERT: A 578 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 753 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5730 (ppp) REVERT: A 772 MET cc_start: 0.8237 (mtt) cc_final: 0.7805 (mmt) REVERT: B 89 ASN cc_start: 0.8904 (m-40) cc_final: 0.7685 (m110) REVERT: B 373 LEU cc_start: 0.8607 (tp) cc_final: 0.8346 (pp) REVERT: B 515 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8246 (mm) REVERT: B 579 MET cc_start: 0.8128 (tpp) cc_final: 0.7659 (tmm) REVERT: B 587 TRP cc_start: 0.8249 (m-10) cc_final: 0.7799 (m-10) REVERT: B 605 TRP cc_start: 0.8713 (m100) cc_final: 0.7835 (m100) REVERT: B 607 PHE cc_start: 0.8527 (t80) cc_final: 0.7859 (t80) REVERT: B 648 ASP cc_start: 0.8211 (t0) cc_final: 0.7873 (t0) REVERT: B 832 HIS cc_start: 0.8250 (t-170) cc_final: 0.7839 (t-170) outliers start: 36 outliers final: 29 residues processed: 172 average time/residue: 0.1105 time to fit residues: 28.5604 Evaluate side-chains 176 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 817 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 76 optimal weight: 0.1980 chunk 120 optimal weight: 7.9990 chunk 146 optimal weight: 40.0000 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 722 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 = 0.4220 r_free = 0.4220 target = 0.166863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106666 restraints weight = 24728.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107269 restraints weight = 13906.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107272 restraints weight = 10750.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107754 restraints weight = 9900.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108071 restraints weight = 9122.523| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14810 Z= 0.130 Angle : 0.603 12.224 20430 Z= 0.297 Chirality : 0.038 0.182 2430 Planarity : 0.005 0.066 2285 Dihedral : 17.409 149.659 3108 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.87 % Allowed : 22.25 % Favored : 74.88 % 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 are not related in a simple way. whole: 2.54 (0.21), residues: 1637 helix: 2.48 (0.16), residues: 1077 sheet: 1.27 (0.49), residues: 111 loop : -0.19 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 401 TYR 0.029 0.002 TYR B 817 PHE 0.024 0.001 PHE A 855 TRP 0.025 0.002 TRP A 222 HIS 0.002 0.000 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14808) covalent geometry : angle 0.60292 / 0.30 (20430) hydrogen bonds : bond 0.04034 / 2.75 ( 973) hydrogen bonds : angle 3.89688 / 2.89 ( 2734) Misc. bond : bond 0.00013 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.80 seconds wall clock time: 37 minutes 44.41 seconds (2264.41 seconds total)