Starting phenix.real_space_refine on Fri Jul 3 07:55:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.map" model { file = "/net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w50_65648/07_2026/9w50_65648.cif" } resolution = 3.3 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= -0.002 sd= 0.059 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 4 5.49 5 S 46 5.16 5 C 8194 2.51 5 N 2140 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12502 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6149 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 43, 'TRANS': 758} Chain breaks: 2 Chain: "B" Number of atoms: 6149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6149 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 43, 'TRANS': 758} Chain breaks: 2 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'PGT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.19 Number of scatterers: 12502 At special positions: 0 Unit cell: (118.77, 114.49, 121.98, 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 46 16.00 P 4 15.00 O 2118 8.00 N 2140 7.00 C 8194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS B 389 " distance=2.05 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS B 386 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 425.7 milliseconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 68.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 33 through 54 Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.787A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.504A pdb=" N LEU A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 125 removed outlier: 3.808A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 145 through 174 removed outlier: 3.900A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.532A pdb=" N HIS A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 262 removed outlier: 3.651A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.883A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.578A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 355 through 377 removed outlier: 3.944A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 removed outlier: 3.947A pdb=" N CYS A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 390 " --> pdb=" O CYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.751A pdb=" N ASP A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 444 removed outlier: 3.683A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 462 removed outlier: 3.514A pdb=" N PHE A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 500 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.920A pdb=" N TRP A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 511 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 553 through 566 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 610 through 628 removed outlier: 3.763A pdb=" N GLU A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 672 through 689 Processing helix chain 'A' and resid 701 through 715 removed outlier: 3.522A pdb=" N GLY A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.835A pdb=" N PHE A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE A 736 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 793 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.787A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 102 removed outlier: 3.504A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 125 removed outlier: 3.808A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 145 through 174 removed outlier: 3.900A pdb=" N LEU B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.532A pdb=" N HIS B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 262 removed outlier: 3.651A pdb=" N LEU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.883A pdb=" N LEU B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.578A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 345 Processing helix chain 'B' and resid 355 through 377 removed outlier: 3.944A pdb=" N ILE B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 391 removed outlier: 3.947A pdb=" N CYS B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 390 " --> pdb=" O CYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 removed outlier: 3.751A pdb=" N ASP B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 444 removed outlier: 3.683A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 462 removed outlier: 3.514A pdb=" N PHE B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 500 Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.920A pdb=" N TRP B 510 " --> pdb=" O ASN B 507 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 511 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 553 through 566 Processing helix chain 'B' and resid 570 through 576 Processing helix chain 'B' and resid 610 through 628 removed outlier: 3.762A pdb=" N GLU B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 622 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 641 through 649 Processing helix chain 'B' and resid 672 through 689 Processing helix chain 'B' and resid 701 through 715 removed outlier: 3.521A pdb=" N GLY B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.836A pdb=" N PHE B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 736 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 793 Processing helix chain 'B' and resid 835 through 842 Processing helix chain 'B' and resid 861 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.277A pdb=" N MET A 601 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 635 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA A 603 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 637 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR A 635 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A 853 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 656 " --> pdb=" O ARG A 850 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 852 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS A 654 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 854 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA A 652 " --> pdb=" O VAL A 854 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 661 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 798 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 762 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLY A 800 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N LEU A 764 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN A 752 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET A 767 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE A 750 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS A 743 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 749 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'B' and resid 581 through 584 removed outlier: 6.277A pdb=" N MET B 601 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR B 635 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 603 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 637 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR B 635 " --> pdb=" O ALA B 853 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 853 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 656 " --> pdb=" O ARG B 850 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU B 852 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS B 654 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 854 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA B 652 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 661 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 798 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 762 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLY B 800 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N LEU B 764 " --> pdb=" O GLY B 800 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 752 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N MET B 767 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 750 " --> pdb=" O MET B 767 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS B 743 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 749 " --> pdb=" O VAL B 741 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2245 1.33 - 1.45: 2991 1.45 - 1.57: 7460 1.57 - 1.69: 8 1.69 - 1.82: 72 Bond restraints: 12776 Sorted by residual: bond pdb=" C1 PGT B 901 " pdb=" O3P PGT B 901 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C1 PGT A 901 " pdb=" O3P PGT A 901 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C4 PGT A 903 " pdb=" O4P PGT A 903 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C4 PGT A 902 " pdb=" O4P PGT A 902 " ideal model delta sigma weight residual 1.410 1.457 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" C THR B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.25e-02 6.40e+03 4.86e+00 ... (remaining 12771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 15780 1.85 - 3.71: 1515 3.71 - 5.56: 47 5.56 - 7.41: 0 7.41 - 9.27: 4 Bond angle restraints: 17346 Sorted by residual: angle pdb=" CA ASP A 647 " pdb=" CB ASP A 647 " pdb=" CG ASP A 647 " ideal model delta sigma weight residual 112.60 116.64 -4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" CA ASP B 647 " pdb=" CB ASP B 647 " pdb=" CG ASP B 647 " ideal model delta sigma weight residual 112.60 116.58 -3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CA ASP B 757 " pdb=" CB ASP B 757 " pdb=" CG ASP B 757 " ideal model delta sigma weight residual 112.60 116.55 -3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " pdb=" CG ASP A 757 " ideal model delta sigma weight residual 112.60 116.53 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" CA ASP B 662 " pdb=" CB ASP B 662 " pdb=" CG ASP B 662 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.53e+01 ... (remaining 17341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 6786 15.80 - 31.61: 619 31.61 - 47.41: 151 47.41 - 63.21: 53 63.21 - 79.02: 15 Dihedral angle restraints: 7624 sinusoidal: 3012 harmonic: 4612 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -42.71 -43.29 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS B 389 " pdb=" CB CYS B 389 " ideal model delta sinusoidal sigma weight residual -86.00 -42.73 -43.27 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA CYS B 389 " pdb=" C CYS B 389 " pdb=" N LEU B 390 " pdb=" CA LEU B 390 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1189 0.040 - 0.080: 476 0.080 - 0.121: 277 0.121 - 0.161: 70 0.161 - 0.201: 16 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" C PRO A 288 " pdb=" CB PRO A 288 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO B 288 " pdb=" N PRO B 288 " pdb=" C PRO B 288 " pdb=" CB PRO B 288 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL B 124 " pdb=" CA VAL B 124 " pdb=" CG1 VAL B 124 " pdb=" CG2 VAL B 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2025 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 419 " 0.183 9.50e-02 1.11e+02 8.21e-02 4.37e+00 pdb=" NE ARG A 419 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 419 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 419 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 419 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 419 " -0.183 9.50e-02 1.11e+02 8.20e-02 4.36e+00 pdb=" NE ARG B 419 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 419 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 419 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 419 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PGT A 901 " 0.035 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C12 PGT A 901 " -0.010 2.00e-02 2.50e+03 pdb=" O11 PGT A 901 " -0.014 2.00e-02 2.50e+03 pdb=" O3 PGT A 901 " -0.011 2.00e-02 2.50e+03 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 4872 2.94 - 3.43: 13219 3.43 - 3.92: 20254 3.92 - 4.41: 22259 4.41 - 4.90: 37599 Nonbonded interactions: 98203 Sorted by model distance: nonbonded pdb=" O2 PGT A 902 " pdb=" O3 PGT A 902 " model vdw 2.456 2.432 nonbonded pdb=" O2 PGT A 903 " pdb=" O3 PGT A 903 " model vdw 2.457 2.432 nonbonded pdb=" O GLY B 282 " pdb=" OG SER B 285 " model vdw 2.492 3.040 nonbonded pdb=" O GLY A 282 " pdb=" OG SER A 285 " model vdw 2.492 3.040 nonbonded pdb=" O PHE B 723 " pdb=" OG SER B 724 " model vdw 2.542 3.040 ... (remaining 98198 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 33 through 901) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.430 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 0.048 12778 Z= 0.482 Angle : 1.111 9.269 17350 Z= 0.789 Chirality : 0.057 0.201 2028 Planarity : 0.005 0.082 2170 Dihedral : 13.931 79.018 4642 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.11 % Rotamer: Outliers : 1.12 % Allowed : 8.48 % Favored : 90.40 % 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: -0.57 (0.19), residues: 1592 helix: 0.32 (0.15), residues: 1026 sheet: -0.51 (0.37), residues: 156 loop : -1.89 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 420 TYR 0.018 0.003 TYR B 136 PHE 0.021 0.002 PHE B 355 TRP 0.019 0.002 TRP A 619 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.48 (12776) covalent geometry : angle 1.11101 / 0.79 (17346) SS BOND : bond 0.01530 / 0.77 ( 2) SS BOND : angle 0.82842 / 0.44 ( 4) hydrogen bonds : bond 0.14801 / 10.24 ( 847) hydrogen bonds : angle 6.30521 / 4.68 ( 2481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.394 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: A 129 LEU cc_start: 0.8406 (tp) cc_final: 0.8073 (tp) REVERT: A 355 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 752 ASN cc_start: 0.8601 (t0) cc_final: 0.7640 (t0) REVERT: A 840 LYS cc_start: 0.9163 (mttp) cc_final: 0.8957 (mttt) REVERT: A 842 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8463 (pttt) REVERT: B 129 LEU cc_start: 0.8407 (tp) cc_final: 0.8074 (tp) REVERT: B 355 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8308 (t80) REVERT: B 840 LYS cc_start: 0.9163 (mttp) cc_final: 0.8957 (mttt) REVERT: B 842 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8462 (pttt) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.0986 time to fit residues: 20.3140 Evaluate side-chains 77 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.053196 restraints weight = 46886.048| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.93 r_work: 0.2813 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12778 Z= 0.142 Angle : 0.554 10.032 17350 Z= 0.267 Chirality : 0.036 0.175 2028 Planarity : 0.004 0.032 2170 Dihedral : 7.209 59.099 1912 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 11.68 % Favored : 85.68 % 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: 1.74 (0.21), residues: 1592 helix: 2.25 (0.16), residues: 1040 sheet: -0.02 (0.38), residues: 156 loop : -1.43 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.019 0.001 TYR B 93 PHE 0.016 0.001 PHE B 87 TRP 0.010 0.001 TRP B 425 HIS 0.003 0.001 HIS B 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12776) covalent geometry : angle 0.55390 / 0.27 (17346) SS BOND : bond 0.00042 / 0.02 ( 2) SS BOND : angle 1.19249 / 0.64 ( 4) hydrogen bonds : bond 0.04106 / 2.83 ( 847) hydrogen bonds : angle 4.28377 / 3.16 ( 2481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8357 (tp) cc_final: 0.7857 (tp) REVERT: A 355 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 410 CYS cc_start: 0.9118 (m) cc_final: 0.8910 (m) REVERT: A 683 ASN cc_start: 0.9385 (m110) cc_final: 0.9162 (p0) REVERT: A 752 ASN cc_start: 0.7588 (t0) cc_final: 0.7304 (t0) REVERT: A 783 LEU cc_start: 0.9631 (tp) cc_final: 0.9409 (tp) REVERT: B 129 LEU cc_start: 0.8349 (tp) cc_final: 0.7853 (tp) REVERT: B 355 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8199 (t80) REVERT: B 410 CYS cc_start: 0.9121 (m) cc_final: 0.8917 (m) REVERT: B 683 ASN cc_start: 0.9384 (m110) cc_final: 0.9159 (p0) REVERT: B 752 ASN cc_start: 0.7670 (t0) cc_final: 0.7257 (t0) REVERT: B 783 LEU cc_start: 0.9648 (tp) cc_final: 0.9414 (tp) outliers start: 33 outliers final: 16 residues processed: 100 average time/residue: 0.0660 time to fit residues: 11.1581 Evaluate side-chains 72 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.071992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053804 restraints weight = 46736.433| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.83 r_work: 0.2840 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12778 Z= 0.108 Angle : 0.521 8.959 17350 Z= 0.245 Chirality : 0.036 0.167 2028 Planarity : 0.004 0.041 2170 Dihedral : 6.529 59.223 1904 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.80 % Allowed : 12.08 % Favored : 85.12 % 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: 2.31 (0.21), residues: 1592 helix: 2.63 (0.16), residues: 1040 sheet: 0.20 (0.37), residues: 160 loop : -1.00 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.019 0.001 TYR B 93 PHE 0.012 0.001 PHE A 87 TRP 0.006 0.001 TRP B 425 HIS 0.002 0.001 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12776) covalent geometry : angle 0.52094 / 0.24 (17346) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 1.08833 / 0.58 ( 4) hydrogen bonds : bond 0.03484 / 2.40 ( 847) hydrogen bonds : angle 3.96295 / 2.90 ( 2481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 129 LEU cc_start: 0.8345 (tp) cc_final: 0.7928 (tp) REVERT: A 241 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9169 (tp) REVERT: A 355 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 395 LEU cc_start: 0.8719 (tp) cc_final: 0.8368 (tp) REVERT: A 410 CYS cc_start: 0.8955 (m) cc_final: 0.8754 (m) REVERT: A 683 ASN cc_start: 0.9410 (m110) cc_final: 0.9168 (p0) REVERT: B 77 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 129 LEU cc_start: 0.8346 (tp) cc_final: 0.7930 (tp) REVERT: B 241 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9168 (tp) REVERT: B 355 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 395 LEU cc_start: 0.8712 (tp) cc_final: 0.8360 (tp) REVERT: B 410 CYS cc_start: 0.8950 (m) cc_final: 0.8749 (m) REVERT: B 683 ASN cc_start: 0.9410 (m110) cc_final: 0.9171 (p0) REVERT: B 752 ASN cc_start: 0.7605 (t0) cc_final: 0.7082 (t0) REVERT: B 783 LEU cc_start: 0.9563 (tp) cc_final: 0.9334 (tp) outliers start: 35 outliers final: 20 residues processed: 103 average time/residue: 0.0846 time to fit residues: 14.2968 Evaluate side-chains 88 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050336 restraints weight = 47881.324| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.82 r_work: 0.2750 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12778 Z= 0.224 Angle : 0.613 8.401 17350 Z= 0.289 Chirality : 0.038 0.156 2028 Planarity : 0.004 0.045 2170 Dihedral : 6.845 59.279 1900 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.72 % Allowed : 14.48 % Favored : 82.80 % 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: 2.29 (0.21), residues: 1592 helix: 2.55 (0.16), residues: 1048 sheet: 0.59 (0.39), residues: 156 loop : -1.10 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 420 TYR 0.020 0.001 TYR B 93 PHE 0.019 0.001 PHE B 87 TRP 0.007 0.001 TRP B 425 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (12776) covalent geometry : angle 0.61271 / 0.29 (17346) SS BOND : bond 0.00447 / 0.22 ( 2) SS BOND : angle 1.53096 / 0.74 ( 4) hydrogen bonds : bond 0.04363 / 2.98 ( 847) hydrogen bonds : angle 4.19084 / 3.06 ( 2481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8766 (tt) REVERT: A 129 LEU cc_start: 0.8528 (tp) cc_final: 0.8197 (tp) REVERT: A 241 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9113 (tt) REVERT: A 355 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 602 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9284 (mm) REVERT: A 683 ASN cc_start: 0.9418 (m110) cc_final: 0.9162 (p0) REVERT: A 761 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 767 MET cc_start: 0.7852 (tmm) cc_final: 0.7411 (tmm) REVERT: B 77 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8766 (tt) REVERT: B 129 LEU cc_start: 0.8530 (tp) cc_final: 0.8201 (tp) REVERT: B 241 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9114 (tt) REVERT: B 355 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8239 (t80) REVERT: B 602 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9285 (mm) REVERT: B 683 ASN cc_start: 0.9413 (m110) cc_final: 0.9161 (p0) REVERT: B 752 ASN cc_start: 0.7689 (t0) cc_final: 0.7196 (t0) REVERT: B 761 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 767 MET cc_start: 0.7863 (tmm) cc_final: 0.7392 (tmm) REVERT: B 783 LEU cc_start: 0.9624 (tp) cc_final: 0.9415 (tp) outliers start: 34 outliers final: 21 residues processed: 89 average time/residue: 0.0846 time to fit residues: 12.0971 Evaluate side-chains 83 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.070782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.052711 restraints weight = 47211.799| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.84 r_work: 0.2821 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12778 Z= 0.107 Angle : 0.525 8.909 17350 Z= 0.248 Chirality : 0.036 0.151 2028 Planarity : 0.004 0.045 2170 Dihedral : 6.467 58.795 1900 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.20 % Allowed : 14.08 % Favored : 82.72 % 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: 2.63 (0.21), residues: 1592 helix: 2.86 (0.16), residues: 1030 sheet: 0.72 (0.38), residues: 156 loop : -0.90 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.017 0.001 TYR A 93 PHE 0.012 0.001 PHE A 87 TRP 0.005 0.001 TRP B 446 HIS 0.002 0.000 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (12776) covalent geometry : angle 0.52472 / 0.25 (17346) SS BOND : bond 0.00168 / 0.08 ( 2) SS BOND : angle 1.02032 / 0.53 ( 4) hydrogen bonds : bond 0.03392 / 2.32 ( 847) hydrogen bonds : angle 3.84521 / 2.81 ( 2481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 63 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 107 MET cc_start: 0.8004 (mpp) cc_final: 0.7742 (mmp) REVERT: A 129 LEU cc_start: 0.8422 (tp) cc_final: 0.8137 (tp) REVERT: A 241 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9193 (tp) REVERT: A 355 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 612 MET cc_start: 0.8993 (pmm) cc_final: 0.8675 (pmm) REVERT: A 683 ASN cc_start: 0.9426 (m110) cc_final: 0.9154 (p0) REVERT: A 761 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8264 (tt) REVERT: A 767 MET cc_start: 0.7831 (tmm) cc_final: 0.7343 (tmm) REVERT: B 77 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 107 MET cc_start: 0.8006 (mpp) cc_final: 0.7741 (mmp) REVERT: B 129 LEU cc_start: 0.8417 (tp) cc_final: 0.8133 (tp) REVERT: B 241 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9195 (tp) REVERT: B 355 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8348 (t80) REVERT: B 612 MET cc_start: 0.8997 (pmm) cc_final: 0.8683 (pmm) REVERT: B 683 ASN cc_start: 0.9411 (m110) cc_final: 0.9142 (p0) REVERT: B 761 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8278 (tt) REVERT: B 767 MET cc_start: 0.7830 (tmm) cc_final: 0.7344 (tmm) REVERT: B 783 LEU cc_start: 0.9601 (tp) cc_final: 0.9395 (tp) outliers start: 40 outliers final: 23 residues processed: 102 average time/residue: 0.0744 time to fit residues: 12.6785 Evaluate side-chains 91 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050691 restraints weight = 47571.030| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.82 r_work: 0.2765 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12778 Z= 0.176 Angle : 0.582 9.390 17350 Z= 0.271 Chirality : 0.037 0.145 2028 Planarity : 0.004 0.046 2170 Dihedral : 6.543 59.285 1900 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.52 % Allowed : 13.84 % Favored : 82.64 % 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: 2.55 (0.21), residues: 1592 helix: 2.66 (0.16), residues: 1056 sheet: 0.80 (0.38), residues: 158 loop : -0.84 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 742 TYR 0.018 0.001 TYR B 93 PHE 0.017 0.001 PHE B 87 TRP 0.005 0.001 TRP B 425 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (12776) covalent geometry : angle 0.58188 / 0.27 (17346) SS BOND : bond 0.00390 / 0.20 ( 2) SS BOND : angle 1.29641 / 0.64 ( 4) hydrogen bonds : bond 0.03955 / 2.70 ( 847) hydrogen bonds : angle 4.00918 / 2.93 ( 2481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 58 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 107 MET cc_start: 0.8022 (mpp) cc_final: 0.7773 (mmp) REVERT: A 129 LEU cc_start: 0.8543 (tp) cc_final: 0.8276 (tp) REVERT: A 241 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9142 (tt) REVERT: A 355 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8381 (t80) REVERT: A 612 MET cc_start: 0.9028 (pmm) cc_final: 0.8710 (pmm) REVERT: A 683 ASN cc_start: 0.9425 (m110) cc_final: 0.9155 (p0) REVERT: A 761 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 767 MET cc_start: 0.7855 (tmm) cc_final: 0.7391 (tmm) REVERT: B 77 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8732 (tt) REVERT: B 107 MET cc_start: 0.8021 (mpp) cc_final: 0.7771 (mmp) REVERT: B 129 LEU cc_start: 0.8543 (tp) cc_final: 0.8279 (tp) REVERT: B 241 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9142 (tt) REVERT: B 355 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 612 MET cc_start: 0.9028 (pmm) cc_final: 0.8705 (pmm) REVERT: B 683 ASN cc_start: 0.9420 (m110) cc_final: 0.9146 (p0) REVERT: B 752 ASN cc_start: 0.7758 (t0) cc_final: 0.7495 (t0) REVERT: B 761 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8339 (tt) REVERT: B 767 MET cc_start: 0.7887 (tmm) cc_final: 0.7398 (tmm) outliers start: 44 outliers final: 28 residues processed: 99 average time/residue: 0.0796 time to fit residues: 13.0922 Evaluate side-chains 91 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 55 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051693 restraints weight = 46965.169| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.83 r_work: 0.2793 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12778 Z= 0.130 Angle : 0.544 10.017 17350 Z= 0.254 Chirality : 0.036 0.141 2028 Planarity : 0.004 0.047 2170 Dihedral : 6.368 59.032 1900 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.44 % Allowed : 14.88 % Favored : 81.68 % 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: 2.75 (0.21), residues: 1592 helix: 2.89 (0.16), residues: 1032 sheet: 0.84 (0.39), residues: 156 loop : -0.72 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 638 TYR 0.017 0.001 TYR A 93 PHE 0.014 0.001 PHE A 87 TRP 0.005 0.001 TRP A 446 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12776) covalent geometry : angle 0.54375 / 0.25 (17346) SS BOND : bond 0.00282 / 0.14 ( 2) SS BOND : angle 1.08612 / 0.55 ( 4) hydrogen bonds : bond 0.03543 / 2.42 ( 847) hydrogen bonds : angle 3.86981 / 2.83 ( 2481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 61 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8575 (p0) REVERT: A 77 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 107 MET cc_start: 0.8016 (mpp) cc_final: 0.7782 (mmp) REVERT: A 129 LEU cc_start: 0.8507 (tp) cc_final: 0.8249 (tp) REVERT: A 355 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8488 (t80) REVERT: A 612 MET cc_start: 0.9034 (pmm) cc_final: 0.8730 (pmm) REVERT: A 683 ASN cc_start: 0.9429 (m110) cc_final: 0.9152 (p0) REVERT: A 761 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8328 (tt) REVERT: A 767 MET cc_start: 0.7866 (tmm) cc_final: 0.7399 (tmm) REVERT: B 77 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8715 (tt) REVERT: B 107 MET cc_start: 0.8018 (mpp) cc_final: 0.7780 (mmp) REVERT: B 129 LEU cc_start: 0.8509 (tp) cc_final: 0.8254 (tp) REVERT: B 355 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8484 (t80) REVERT: B 612 MET cc_start: 0.9023 (pmm) cc_final: 0.8716 (pmm) REVERT: B 683 ASN cc_start: 0.9421 (m110) cc_final: 0.9148 (p0) REVERT: B 752 ASN cc_start: 0.7750 (t0) cc_final: 0.7470 (t0) REVERT: B 761 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8345 (tt) REVERT: B 767 MET cc_start: 0.7788 (tmm) cc_final: 0.7335 (tmm) outliers start: 43 outliers final: 29 residues processed: 103 average time/residue: 0.0730 time to fit residues: 12.5155 Evaluate side-chains 94 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052049 restraints weight = 46740.558| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.81 r_work: 0.2808 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12778 Z= 0.118 Angle : 0.563 10.767 17350 Z= 0.257 Chirality : 0.036 0.139 2028 Planarity : 0.004 0.047 2170 Dihedral : 6.260 59.208 1900 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.44 % Allowed : 14.88 % Favored : 81.68 % 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: 2.74 (0.21), residues: 1592 helix: 2.81 (0.16), residues: 1052 sheet: 0.88 (0.39), residues: 156 loop : -0.75 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 420 TYR 0.017 0.001 TYR A 93 PHE 0.014 0.001 PHE B 87 TRP 0.005 0.001 TRP A 446 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12776) covalent geometry : angle 0.56323 / 0.26 (17346) SS BOND : bond 0.00266 / 0.13 ( 2) SS BOND : angle 0.99653 / 0.51 ( 4) hydrogen bonds : bond 0.03431 / 2.33 ( 847) hydrogen bonds : angle 3.82603 / 2.80 ( 2481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 107 MET cc_start: 0.8029 (mpp) cc_final: 0.7799 (mmp) REVERT: A 129 LEU cc_start: 0.8499 (tp) cc_final: 0.8237 (tp) REVERT: A 355 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8491 (t80) REVERT: A 612 MET cc_start: 0.9002 (pmm) cc_final: 0.8712 (pmm) REVERT: A 683 ASN cc_start: 0.9430 (m110) cc_final: 0.9152 (p0) REVERT: A 761 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 767 MET cc_start: 0.7775 (tmm) cc_final: 0.7280 (tmm) REVERT: B 60 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8464 (p0) REVERT: B 77 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 107 MET cc_start: 0.8039 (mpp) cc_final: 0.7801 (mmp) REVERT: B 129 LEU cc_start: 0.8507 (tp) cc_final: 0.8247 (tp) REVERT: B 355 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8489 (t80) REVERT: B 612 MET cc_start: 0.8986 (pmm) cc_final: 0.8700 (pmm) REVERT: B 683 ASN cc_start: 0.9416 (m110) cc_final: 0.9139 (p0) REVERT: B 752 ASN cc_start: 0.7701 (t0) cc_final: 0.7412 (t0) REVERT: B 761 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 767 MET cc_start: 0.7796 (tmm) cc_final: 0.7339 (tmm) outliers start: 43 outliers final: 27 residues processed: 103 average time/residue: 0.0687 time to fit residues: 11.9289 Evaluate side-chains 92 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 159 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052836 restraints weight = 46979.784| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.82 r_work: 0.2829 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12778 Z= 0.103 Angle : 0.546 10.921 17350 Z= 0.250 Chirality : 0.036 0.140 2028 Planarity : 0.004 0.047 2170 Dihedral : 6.083 59.568 1900 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.20 % Allowed : 14.88 % Favored : 81.92 % 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: 2.77 (0.21), residues: 1592 helix: 2.85 (0.16), residues: 1054 sheet: 0.80 (0.39), residues: 166 loop : -0.78 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 638 TYR 0.015 0.001 TYR A 93 PHE 0.012 0.001 PHE A 87 TRP 0.006 0.001 TRP A 446 HIS 0.002 0.000 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (12776) covalent geometry : angle 0.54541 / 0.25 (17346) SS BOND : bond 0.00216 / 0.11 ( 2) SS BOND : angle 0.94869 / 0.50 ( 4) hydrogen bonds : bond 0.03178 / 2.16 ( 847) hydrogen bonds : angle 3.74251 / 2.74 ( 2481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 63 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 107 MET cc_start: 0.8011 (mpp) cc_final: 0.7799 (mmp) REVERT: A 129 LEU cc_start: 0.8428 (tp) cc_final: 0.8196 (tp) REVERT: A 355 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8765 (t80) REVERT: A 612 MET cc_start: 0.8978 (pmm) cc_final: 0.8719 (pmm) REVERT: A 683 ASN cc_start: 0.9424 (m110) cc_final: 0.9142 (p0) REVERT: A 761 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 782 MET cc_start: 0.9416 (ptm) cc_final: 0.9111 (ppp) REVERT: B 60 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8432 (p0) REVERT: B 77 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8715 (tt) REVERT: B 107 MET cc_start: 0.8025 (mpp) cc_final: 0.7804 (mmp) REVERT: B 129 LEU cc_start: 0.8433 (tp) cc_final: 0.8200 (tp) REVERT: B 355 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8766 (t80) REVERT: B 602 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9343 (mm) REVERT: B 612 MET cc_start: 0.8976 (pmm) cc_final: 0.8733 (pmm) REVERT: B 683 ASN cc_start: 0.9403 (m110) cc_final: 0.9128 (p0) REVERT: B 761 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 767 MET cc_start: 0.7796 (tmm) cc_final: 0.7297 (tmm) outliers start: 40 outliers final: 29 residues processed: 102 average time/residue: 0.0775 time to fit residues: 12.6749 Evaluate side-chains 96 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 92 optimal weight: 0.0170 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 131 optimal weight: 0.0270 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053418 restraints weight = 47077.578| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.82 r_work: 0.2847 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12778 Z= 0.096 Angle : 0.553 11.804 17350 Z= 0.252 Chirality : 0.036 0.140 2028 Planarity : 0.004 0.047 2170 Dihedral : 5.954 59.972 1900 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 15.36 % Favored : 81.84 % 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: 2.93 (0.21), residues: 1592 helix: 2.98 (0.16), residues: 1044 sheet: 1.11 (0.40), residues: 160 loop : -0.75 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 524 TYR 0.015 0.001 TYR B 93 PHE 0.012 0.001 PHE A 87 TRP 0.005 0.000 TRP A 446 HIS 0.002 0.000 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (12776) covalent geometry : angle 0.55325 / 0.25 (17346) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.93884 / 0.50 ( 4) hydrogen bonds : bond 0.03108 / 2.15 ( 847) hydrogen bonds : angle 3.68717 / 2.69 ( 2481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8374 (p0) REVERT: A 77 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 129 LEU cc_start: 0.8435 (tp) cc_final: 0.8186 (tp) REVERT: A 355 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8641 (t80) REVERT: A 612 MET cc_start: 0.8976 (pmm) cc_final: 0.8744 (pmm) REVERT: A 683 ASN cc_start: 0.9417 (m110) cc_final: 0.9142 (p0) REVERT: A 761 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 782 MET cc_start: 0.9413 (ptm) cc_final: 0.9114 (ppp) REVERT: B 60 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8383 (p0) REVERT: B 77 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (tt) REVERT: B 107 MET cc_start: 0.8014 (mpp) cc_final: 0.7808 (mmp) REVERT: B 129 LEU cc_start: 0.8440 (tp) cc_final: 0.8198 (tp) REVERT: B 355 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8599 (t80) REVERT: B 612 MET cc_start: 0.8956 (pmm) cc_final: 0.8731 (pmm) REVERT: B 683 ASN cc_start: 0.9398 (m110) cc_final: 0.9124 (p0) REVERT: B 761 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 767 MET cc_start: 0.7719 (tmm) cc_final: 0.7229 (tmm) outliers start: 35 outliers final: 23 residues processed: 91 average time/residue: 0.0700 time to fit residues: 10.4425 Evaluate side-chains 85 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 540 TRP Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053795 restraints weight = 47028.983| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.81 r_work: 0.2857 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12778 Z= 0.094 Angle : 0.564 11.721 17350 Z= 0.253 Chirality : 0.036 0.144 2028 Planarity : 0.004 0.047 2170 Dihedral : 5.861 59.984 1900 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.56 % Allowed : 15.68 % Favored : 81.76 % 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: 3.01 (0.21), residues: 1592 helix: 3.02 (0.15), residues: 1048 sheet: 1.10 (0.40), residues: 160 loop : -0.69 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 524 TYR 0.015 0.001 TYR B 93 PHE 0.011 0.001 PHE A 87 TRP 0.006 0.000 TRP A 446 HIS 0.002 0.000 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (12776) covalent geometry : angle 0.56365 / 0.25 (17346) SS BOND : bond 0.00229 / 0.12 ( 2) SS BOND : angle 0.90878 / 0.48 ( 4) hydrogen bonds : bond 0.02998 / 2.06 ( 847) hydrogen bonds : angle 3.63255 / 2.65 ( 2481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.45 seconds wall clock time: 38 minutes 15.33 seconds (2295.33 seconds total)