Starting phenix.real_space_refine on Mon Aug 10 03:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.cif Found real_map, /net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.map" model { file = "/net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13he_77065/08_2026/13he_77065.cif" } resolution = 4.07 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 12 5.49 5 S 258 5.16 5 C 25512 2.51 5 N 6666 2.21 5 O 7674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40128 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "B" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "C" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "D" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "E" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "F" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6643 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 823} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.40, per 1000 atoms: 0.18 Number of scatterers: 40128 At special positions: 0 Unit cell: (133.96, 153, 264.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 258 16.00 P 12 15.00 O 7674 8.00 N 6666 7.00 C 25512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9636 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 30 sheets defined 55.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.573A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.870A pdb=" N LYS A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 69 through 88 removed outlier: 3.901A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 150 through 169 removed outlier: 4.097A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 354 through 367 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.218A pdb=" N ILE A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.047A pdb=" N LEU A 445 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.686A pdb=" N ALA A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.516A pdb=" N ARG A 586 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 635 Processing helix chain 'A' and resid 642 through 646 removed outlier: 3.653A pdb=" N MET A 645 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 670 Processing helix chain 'A' and resid 675 through 700 removed outlier: 4.374A pdb=" N SER A 680 " --> pdb=" O ASP A 676 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 703 through 722 Processing helix chain 'A' and resid 728 through 741 removed outlier: 3.725A pdb=" N LYS A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 760 removed outlier: 4.563A pdb=" N ASN A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 790 Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.929A pdb=" N GLU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 843 removed outlier: 4.570A pdb=" N ASP A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.658A pdb=" N THR A 849 " --> pdb=" O CYS A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 869 Processing helix chain 'B' and resid 13 through 32 removed outlier: 3.559A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 removed outlier: 3.961A pdb=" N LYS B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 69 through 88 removed outlier: 3.510A pdb=" N LYS B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 150 through 169 removed outlier: 4.153A pdb=" N THR B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.524A pdb=" N MET B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 354 through 367 Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.214A pdb=" N ILE B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 440 through 445 removed outlier: 4.112A pdb=" N LEU B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.564A pdb=" N MET B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.664A pdb=" N ALA B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.525A pdb=" N ARG B 586 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 635 Processing helix chain 'B' and resid 642 through 646 removed outlier: 3.655A pdb=" N MET B 645 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 670 Processing helix chain 'B' and resid 675 through 700 removed outlier: 4.429A pdb=" N SER B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 681 " --> pdb=" O TYR B 677 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 703 through 722 Processing helix chain 'B' and resid 728 through 741 removed outlier: 3.743A pdb=" N LYS B 735 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 760 removed outlier: 4.527A pdb=" N ASN B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 790 Processing helix chain 'B' and resid 797 through 815 removed outlier: 3.920A pdb=" N GLU B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 826 through 843 removed outlier: 4.517A pdb=" N ASP B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.707A pdb=" N THR B 849 " --> pdb=" O CYS B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 869 Processing helix chain 'C' and resid 13 through 32 removed outlier: 3.573A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.835A pdb=" N LYS C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 69 through 88 removed outlier: 3.504A pdb=" N LYS C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 150 through 169 removed outlier: 4.100A pdb=" N THR C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 354 through 367 Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.210A pdb=" N ILE C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 432 Processing helix chain 'C' and resid 440 through 445 removed outlier: 4.029A pdb=" N LEU C 445 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 478 Processing helix chain 'C' and resid 494 through 500 Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.534A pdb=" N MET C 513 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 543 removed outlier: 3.649A pdb=" N ALA C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 632 through 635 Processing helix chain 'C' and resid 642 through 646 removed outlier: 3.763A pdb=" N MET C 645 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 670 Processing helix chain 'C' and resid 675 through 700 removed outlier: 4.437A pdb=" N SER C 680 " --> pdb=" O ASP C 676 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 681 " --> pdb=" O TYR C 677 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 703 through 722 Processing helix chain 'C' and resid 728 through 741 removed outlier: 3.720A pdb=" N LYS C 735 " --> pdb=" O SER C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 760 removed outlier: 4.596A pdb=" N ASN C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 790 removed outlier: 3.639A pdb=" N ARG C 781 " --> pdb=" O ARG C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 815 removed outlier: 3.948A pdb=" N GLU C 801 " --> pdb=" O GLU C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 826 through 843 removed outlier: 4.556A pdb=" N ASP C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 849 removed outlier: 3.624A pdb=" N THR C 849 " --> pdb=" O CYS C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 869 Processing helix chain 'D' and resid 13 through 32 removed outlier: 3.571A pdb=" N VAL D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 52 removed outlier: 3.884A pdb=" N LYS D 52 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 69 through 88 removed outlier: 3.504A pdb=" N LYS D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 150 through 169 removed outlier: 4.094A pdb=" N THR D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 276 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 354 through 367 Processing helix chain 'D' and resid 385 through 395 Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.263A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'D' and resid 440 through 445 removed outlier: 4.042A pdb=" N LEU D 445 " --> pdb=" O LYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 478 Processing helix chain 'D' and resid 494 through 500 Processing helix chain 'D' and resid 503 through 513 removed outlier: 3.536A pdb=" N MET D 513 " --> pdb=" O LYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 543 removed outlier: 3.684A pdb=" N ALA D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 582 through 586 removed outlier: 3.530A pdb=" N ARG D 586 " --> pdb=" O ILE D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 4.399A pdb=" N VAL D 612 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 613 " --> pdb=" O SER D 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 609 through 613' Processing helix chain 'D' and resid 632 through 635 Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.646A pdb=" N MET D 645 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 Processing helix chain 'D' and resid 675 through 700 removed outlier: 4.394A pdb=" N SER D 680 " --> pdb=" O ASP D 676 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU D 681 " --> pdb=" O TYR D 677 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 703 through 722 Processing helix chain 'D' and resid 728 through 741 removed outlier: 3.717A pdb=" N LYS D 735 " --> pdb=" O SER D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 760 removed outlier: 4.489A pdb=" N ASN D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU D 754 " --> pdb=" O LEU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 790 Processing helix chain 'D' and resid 797 through 815 removed outlier: 3.932A pdb=" N GLU D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 824 Processing helix chain 'D' and resid 826 through 843 removed outlier: 4.580A pdb=" N ASP D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU D 836 " --> pdb=" O ASP D 832 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 849 removed outlier: 3.632A pdb=" N THR D 849 " --> pdb=" O CYS D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 869 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.579A pdb=" N VAL E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.896A pdb=" N LYS E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 69 through 88 removed outlier: 3.886A pdb=" N ILE E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 150 through 169 removed outlier: 4.088A pdb=" N THR E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 204 through 210 Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 264 through 276 Processing helix chain 'E' and resid 281 through 292 Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 336 through 340 Processing helix chain 'E' and resid 354 through 367 Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.620A pdb=" N MET E 395 " --> pdb=" O PHE E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 412 removed outlier: 4.180A pdb=" N ILE E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 440 through 445 removed outlier: 4.039A pdb=" N LEU E 445 " --> pdb=" O LYS E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 478 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 503 through 513 removed outlier: 3.509A pdb=" N MET E 513 " --> pdb=" O LYS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 removed outlier: 3.669A pdb=" N ALA E 532 " --> pdb=" O SER E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 567 Processing helix chain 'E' and resid 572 through 577 Processing helix chain 'E' and resid 582 through 586 removed outlier: 3.525A pdb=" N ARG E 586 " --> pdb=" O ILE E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 613 removed outlier: 4.374A pdb=" N VAL E 612 " --> pdb=" O GLY E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 635 Processing helix chain 'E' and resid 642 through 646 removed outlier: 3.672A pdb=" N MET E 645 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 670 Processing helix chain 'E' and resid 675 through 700 removed outlier: 4.429A pdb=" N SER E 680 " --> pdb=" O ASP E 676 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU E 681 " --> pdb=" O TYR E 677 " (cutoff:3.500A) Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 703 through 722 Processing helix chain 'E' and resid 728 through 741 removed outlier: 3.724A pdb=" N LYS E 735 " --> pdb=" O SER E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 760 removed outlier: 4.554A pdb=" N ASN E 753 " --> pdb=" O ALA E 749 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU E 754 " --> pdb=" O LEU E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 790 removed outlier: 3.643A pdb=" N ARG E 781 " --> pdb=" O ARG E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 815 removed outlier: 3.932A pdb=" N GLU E 801 " --> pdb=" O GLU E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 819 through 824 Processing helix chain 'E' and resid 826 through 843 removed outlier: 4.546A pdb=" N ASP E 835 " --> pdb=" O LEU E 831 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP E 843 " --> pdb=" O GLU E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 849 removed outlier: 3.648A pdb=" N THR E 849 " --> pdb=" O CYS E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 855 through 869 Processing helix chain 'F' and resid 13 through 32 removed outlier: 3.581A pdb=" N VAL F 30 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 52 removed outlier: 3.995A pdb=" N LYS F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 69 through 88 removed outlier: 3.506A pdb=" N LYS F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 150 through 169 removed outlier: 4.111A pdb=" N THR F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 193 Processing helix chain 'F' and resid 204 through 210 Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 264 through 276 Processing helix chain 'F' and resid 281 through 292 Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 336 through 340 Processing helix chain 'F' and resid 354 through 367 Processing helix chain 'F' and resid 385 through 395 Processing helix chain 'F' and resid 405 through 412 removed outlier: 4.213A pdb=" N ILE F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 432 Processing helix chain 'F' and resid 440 through 445 removed outlier: 4.096A pdb=" N LEU F 445 " --> pdb=" O LYS F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 478 Processing helix chain 'F' and resid 494 through 500 Processing helix chain 'F' and resid 503 through 512 Processing helix chain 'F' and resid 528 through 543 removed outlier: 3.655A pdb=" N ALA F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 567 Processing helix chain 'F' and resid 572 through 577 Processing helix chain 'F' and resid 582 through 586 removed outlier: 3.642A pdb=" N LYS F 585 " --> pdb=" O ASP F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 635 Processing helix chain 'F' and resid 642 through 646 removed outlier: 3.656A pdb=" N MET F 645 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 670 Processing helix chain 'F' and resid 675 through 700 removed outlier: 4.454A pdb=" N SER F 680 " --> pdb=" O ASP F 676 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU F 681 " --> pdb=" O TYR F 677 " (cutoff:3.500A) Proline residue: F 694 - end of helix Processing helix chain 'F' and resid 703 through 722 Processing helix chain 'F' and resid 728 through 741 removed outlier: 3.685A pdb=" N LYS F 735 " --> pdb=" O SER F 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 760 removed outlier: 4.569A pdb=" N ASN F 753 " --> pdb=" O ALA F 749 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU F 754 " --> pdb=" O LEU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 790 removed outlier: 3.640A pdb=" N ARG F 781 " --> pdb=" O ARG F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 815 removed outlier: 3.943A pdb=" N GLU F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 819 through 824 Processing helix chain 'F' and resid 826 through 843 removed outlier: 4.561A pdb=" N ASP F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU F 836 " --> pdb=" O ASP F 832 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP F 843 " --> pdb=" O GLU F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 845 through 849 removed outlier: 3.630A pdb=" N THR F 849 " --> pdb=" O CYS F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 855 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.683A pdb=" N VAL A 96 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA A 109 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU A 98 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE B 400 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 449 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL B 402 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA A 451 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 375 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 401 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N TYR B 378 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 226 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 261 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 258 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA B 352 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 260 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 325 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET B 349 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 327 " --> pdb=" O MET B 349 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ARG B 351 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR B 278 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU B 328 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.361A pdb=" N VAL A 114 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 197 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 116 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 196 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 279 removed outlier: 6.774A pdb=" N TYR A 278 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N GLU A 328 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 325 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET A 349 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 327 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ARG A 351 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 258 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA A 352 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 260 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 261 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR A 378 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 226 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 375 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 401 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 402 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 98 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA B 109 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 96 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 520 removed outlier: 6.957A pdb=" N LYS A 488 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 548 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 490 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 550 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL A 492 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.367A pdb=" N VAL B 114 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 197 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 116 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 196 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'B' and resid 516 through 523 removed outlier: 4.330A pdb=" N ASP B 522 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS B 488 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE B 548 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 490 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 550 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 492 " --> pdb=" O VAL B 550 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 615 through 619 Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 99 removed outlier: 6.656A pdb=" N VAL C 96 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA C 109 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 98 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE D 400 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR C 449 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL D 402 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA C 451 " --> pdb=" O VAL D 402 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 375 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 401 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR D 378 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE D 226 " --> pdb=" O TYR D 378 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 261 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 258 " --> pdb=" O TYR D 350 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA D 352 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL D 260 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 325 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N MET D 349 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY D 327 " --> pdb=" O MET D 349 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ARG D 351 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR D 278 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N GLU D 328 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.363A pdb=" N VAL C 114 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 197 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 116 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 196 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.778A pdb=" N TYR C 278 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLU C 328 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU C 325 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET C 349 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY C 327 " --> pdb=" O MET C 349 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ARG C 351 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 258 " --> pdb=" O TYR C 350 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA C 352 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 260 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 261 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR C 378 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 226 " --> pdb=" O TYR C 378 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 375 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 401 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 451 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 402 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 98 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 109 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 96 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB6, first strand: chain 'C' and resid 516 through 520 removed outlier: 6.965A pdb=" N LYS C 488 " --> pdb=" O THR C 546 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 548 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C 490 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 550 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL C 492 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 551 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 615 through 619 Processing sheet with id=AB8, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.366A pdb=" N VAL D 114 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU D 197 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 116 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE D 196 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AC1, first strand: chain 'D' and resid 516 through 520 removed outlier: 6.975A pdb=" N LYS D 488 " --> pdb=" O THR D 546 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE D 548 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE D 490 " --> pdb=" O ILE D 548 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL D 550 " --> pdb=" O PHE D 490 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL D 492 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 551 " --> pdb=" O ILE D 602 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 615 through 619 Processing sheet with id=AC3, first strand: chain 'E' and resid 96 through 99 removed outlier: 6.684A pdb=" N VAL E 96 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA E 109 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 98 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE F 400 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 449 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL F 402 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA E 451 " --> pdb=" O VAL F 402 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 375 " --> pdb=" O ARG F 399 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 401 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR F 378 " --> pdb=" O PRO F 224 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE F 226 " --> pdb=" O TYR F 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 261 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 258 " --> pdb=" O TYR F 350 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA F 352 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 260 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 325 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET F 349 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY F 327 " --> pdb=" O MET F 349 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ARG F 351 " --> pdb=" O GLY F 327 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR F 278 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLU F 328 " --> pdb=" O TYR F 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.355A pdb=" N VAL E 114 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU E 197 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 116 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE E 196 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 278 through 279 removed outlier: 6.745A pdb=" N TYR E 278 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLU E 328 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 325 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET E 349 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY E 327 " --> pdb=" O MET E 349 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ARG E 351 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 258 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA E 352 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL E 260 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 261 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR E 378 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE E 226 " --> pdb=" O TYR E 378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 375 " --> pdb=" O ARG E 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 401 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 451 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 402 " --> pdb=" O ALA F 451 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 98 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA F 109 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL F 96 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 293 through 294 Processing sheet with id=AC7, first strand: chain 'E' and resid 516 through 520 removed outlier: 6.978A pdb=" N LYS E 488 " --> pdb=" O THR E 546 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE E 548 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE E 490 " --> pdb=" O ILE E 548 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL E 550 " --> pdb=" O PHE E 490 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL E 492 " --> pdb=" O VAL E 550 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 615 through 619 Processing sheet with id=AC9, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.378A pdb=" N VAL F 114 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU F 197 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA F 116 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE F 196 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 293 through 294 Processing sheet with id=AD2, first strand: chain 'F' and resid 516 through 520 removed outlier: 6.916A pdb=" N LYS F 488 " --> pdb=" O THR F 546 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE F 548 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE F 490 " --> pdb=" O ILE F 548 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL F 550 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL F 492 " --> pdb=" O VAL F 550 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 547 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE F 602 " --> pdb=" O ILE F 547 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA F 549 " --> pdb=" O ILE F 602 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 615 through 619 2030 hydrogen bonds defined for protein. 5763 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: 8.70 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13087 1.34 - 1.46: 8684 1.46 - 1.58: 18633 1.58 - 1.70: 24 1.70 - 1.83: 462 Bond restraints: 40890 Sorted by residual: bond pdb=" CA ILE B 55 " pdb=" CB ILE B 55 " ideal model delta sigma weight residual 1.539 1.522 0.017 5.40e-03 3.43e+04 9.76e+00 bond pdb=" CA ILE F 55 " pdb=" CB ILE F 55 " ideal model delta sigma weight residual 1.539 1.529 0.010 5.40e-03 3.43e+04 3.26e+00 bond pdb=" CA ILE D 55 " pdb=" CB ILE D 55 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.77e+00 bond pdb=" CG GLU F 512 " pdb=" CD GLU F 512 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CG LEU C 21 " pdb=" CD1 LEU C 21 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 ... (remaining 40885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 54458 1.81 - 3.63: 730 3.63 - 5.44: 126 5.44 - 7.25: 26 7.25 - 9.07: 16 Bond angle restraints: 55356 Sorted by residual: angle pdb=" C ASP F 511 " pdb=" N GLU F 512 " pdb=" CA GLU F 512 " ideal model delta sigma weight residual 120.72 113.96 6.76 1.67e+00 3.59e-01 1.64e+01 angle pdb=" N GLU F 512 " pdb=" CA GLU F 512 " pdb=" CB GLU F 512 " ideal model delta sigma weight residual 110.39 116.70 -6.31 1.66e+00 3.63e-01 1.45e+01 angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta sigma weight residual 110.16 115.74 -5.58 1.48e+00 4.57e-01 1.42e+01 angle pdb=" C LEU C 480 " pdb=" N LYS C 481 " pdb=" CA LYS C 481 " ideal model delta sigma weight residual 121.54 128.63 -7.09 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C LEU E 480 " pdb=" N LYS E 481 " pdb=" CA LYS E 481 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.06e+00 ... (remaining 55351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 22664 16.11 - 32.22: 1891 32.22 - 48.33: 428 48.33 - 64.44: 109 64.44 - 80.55: 18 Dihedral angle restraints: 25110 sinusoidal: 10116 harmonic: 14994 Sorted by residual: dihedral pdb=" CA MET B 751 " pdb=" C MET B 751 " pdb=" N ILE B 752 " pdb=" CA ILE B 752 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET F 751 " pdb=" C MET F 751 " pdb=" N ILE F 752 " pdb=" CA ILE F 752 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA MET D 751 " pdb=" C MET D 751 " pdb=" N ILE D 752 " pdb=" CA ILE D 752 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 25107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4255 0.035 - 0.070: 1412 0.070 - 0.105: 442 0.105 - 0.140: 184 0.140 - 0.174: 13 Chirality restraints: 6306 Sorted by residual: chirality pdb=" CA GLU C 82 " pdb=" N GLU C 82 " pdb=" C GLU C 82 " pdb=" CB GLU C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA GLU E 82 " pdb=" N GLU E 82 " pdb=" C GLU E 82 " pdb=" CB GLU E 82 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA GLU A 82 " pdb=" N GLU A 82 " pdb=" C GLU A 82 " pdb=" CB GLU A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 6303 not shown) Planarity restraints: 7086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 344 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO C 345 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 344 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO E 345 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 345 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 345 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 344 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 345 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.025 5.00e-02 4.00e+02 ... (remaining 7083 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 734 2.72 - 3.26: 41249 3.26 - 3.81: 62564 3.81 - 4.35: 71065 4.35 - 4.90: 124188 Nonbonded interactions: 299800 Sorted by model distance: nonbonded pdb=" NE2 HIS D 730 " pdb="FE FE D 901 " model vdw 2.170 2.340 nonbonded pdb=" NE2 HIS A 730 " pdb="FE FE A 901 " model vdw 2.182 2.340 nonbonded pdb=" NE2 HIS B 730 " pdb="FE FE B 901 " model vdw 2.184 2.340 nonbonded pdb=" NE2 HIS C 730 " pdb="FE FE C 901 " model vdw 2.185 2.340 nonbonded pdb=" NE2 HIS E 730 " pdb="FE FE E 901 " model vdw 2.211 2.340 ... (remaining 299795 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.270 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: 0.040 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 32.170 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.002 0.043 40890 Z= 0.108 Angle : 0.553 9.069 55356 Z= 0.284 Chirality : 0.042 0.174 6306 Planarity : 0.003 0.046 7086 Dihedral : 12.846 80.547 15474 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.12), residues: 5154 helix: 2.15 (0.11), residues: 2484 sheet: 0.21 (0.19), residues: 762 loop : -0.65 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 191 TYR 0.019 0.001 TYR F 669 PHE 0.016 0.001 PHE C 770 TRP 0.017 0.001 TRP D 459 HIS 0.006 0.001 HIS D 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (40890) covalent geometry : angle 0.55316 / 0.28 (55356) hydrogen bonds : bond 0.14499 / 10.10 ( 2030) hydrogen bonds : angle 4.75825 / 3.43 ( 5763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 722 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9037 (tmm) cc_final: 0.8808 (tpp) REVERT: A 72 ASP cc_start: 0.8729 (m-30) cc_final: 0.8098 (t0) REVERT: A 437 ASP cc_start: 0.9028 (t0) cc_final: 0.8781 (t0) REVERT: A 484 MET cc_start: 0.7905 (mpp) cc_final: 0.7427 (mpp) REVERT: A 578 MET cc_start: 0.7948 (tpt) cc_final: 0.7745 (tpt) REVERT: A 631 ASP cc_start: 0.8353 (t0) cc_final: 0.7857 (t0) REVERT: A 688 MET cc_start: 0.8897 (mmp) cc_final: 0.8105 (mtp) REVERT: A 723 ASN cc_start: 0.7984 (m-40) cc_final: 0.7609 (t0) REVERT: A 837 MET cc_start: 0.8305 (mmm) cc_final: 0.7875 (mmt) REVERT: B 67 MET cc_start: 0.5947 (tmm) cc_final: 0.5600 (tmm) REVERT: B 90 ASN cc_start: 0.8072 (m-40) cc_final: 0.7805 (m-40) REVERT: B 250 MET cc_start: 0.8572 (mtm) cc_final: 0.8066 (ptm) REVERT: B 340 HIS cc_start: 0.8274 (m90) cc_final: 0.7458 (t70) REVERT: B 357 ASP cc_start: 0.8987 (m-30) cc_final: 0.8673 (m-30) REVERT: B 404 THR cc_start: 0.9203 (m) cc_final: 0.8819 (p) REVERT: B 456 ASN cc_start: 0.8121 (t0) cc_final: 0.7917 (t0) REVERT: B 484 MET cc_start: 0.8140 (mpp) cc_final: 0.7617 (mpp) REVERT: B 503 THR cc_start: 0.8995 (p) cc_final: 0.8632 (t) REVERT: B 515 ILE cc_start: 0.8515 (mt) cc_final: 0.8186 (mm) REVERT: B 565 MET cc_start: 0.8508 (ttp) cc_final: 0.8290 (ttp) REVERT: B 631 ASP cc_start: 0.8472 (t0) cc_final: 0.7963 (t0) REVERT: B 843 ASP cc_start: 0.9068 (t0) cc_final: 0.8712 (t0) REVERT: C 45 GLU cc_start: 0.8833 (tp30) cc_final: 0.8573 (tp30) REVERT: C 48 MET cc_start: 0.8810 (tpt) cc_final: 0.8373 (tmm) REVERT: C 287 LYS cc_start: 0.8522 (mttt) cc_final: 0.8201 (mtmt) REVERT: C 380 ASP cc_start: 0.8892 (t0) cc_final: 0.8391 (t0) REVERT: C 437 ASP cc_start: 0.7258 (t0) cc_final: 0.6761 (p0) REVERT: C 484 MET cc_start: 0.6481 (mpp) cc_final: 0.6192 (mpp) REVERT: C 593 MET cc_start: 0.4639 (ttt) cc_final: 0.4002 (ttt) REVERT: C 599 PHE cc_start: 0.7264 (t80) cc_final: 0.6540 (t80) REVERT: C 633 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 638 MET cc_start: 0.8164 (mmp) cc_final: 0.7802 (mmm) REVERT: C 690 PHE cc_start: 0.8531 (t80) cc_final: 0.8304 (m-80) REVERT: C 837 MET cc_start: 0.8322 (mmp) cc_final: 0.8114 (mmm) REVERT: D 60 MET cc_start: 0.8115 (mtp) cc_final: 0.7588 (ttt) REVERT: D 192 GLU cc_start: 0.8267 (tp30) cc_final: 0.7947 (tp30) REVERT: D 275 ARG cc_start: 0.6561 (mmt180) cc_final: 0.6129 (tpp80) REVERT: D 508 ASP cc_start: 0.8328 (m-30) cc_final: 0.8078 (m-30) REVERT: D 571 VAL cc_start: 0.8376 (t) cc_final: 0.8141 (t) REVERT: D 578 MET cc_start: 0.7472 (tpt) cc_final: 0.7115 (mtt) REVERT: D 581 MET cc_start: 0.7841 (pmm) cc_final: 0.7320 (ptp) REVERT: D 631 ASP cc_start: 0.8354 (t0) cc_final: 0.7927 (m-30) REVERT: D 684 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7864 (tpp80) REVERT: D 837 MET cc_start: 0.7980 (mmp) cc_final: 0.5816 (ttp) REVERT: E 53 MET cc_start: 0.8607 (tpt) cc_final: 0.7798 (tpp) REVERT: E 188 LEU cc_start: 0.8513 (mm) cc_final: 0.8101 (mm) REVERT: E 301 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8574 (tmmt) REVERT: E 354 ASP cc_start: 0.8265 (t0) cc_final: 0.7936 (t70) REVERT: E 404 THR cc_start: 0.9209 (m) cc_final: 0.8826 (p) REVERT: E 457 MET cc_start: 0.4022 (tpp) cc_final: 0.3709 (tpp) REVERT: E 538 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8090 (tm-30) REVERT: E 557 ASP cc_start: 0.8878 (m-30) cc_final: 0.8250 (t0) REVERT: E 581 MET cc_start: 0.8111 (mpp) cc_final: 0.7778 (mtt) REVERT: E 593 MET cc_start: 0.8126 (mtp) cc_final: 0.7607 (mtm) REVERT: E 642 ASP cc_start: 0.8243 (t0) cc_final: 0.8031 (t0) REVERT: F 15 GLU cc_start: 0.7570 (mp0) cc_final: 0.6841 (mm-30) REVERT: F 26 GLU cc_start: 0.9208 (pt0) cc_final: 0.8977 (pp20) REVERT: F 395 MET cc_start: 0.7877 (mmp) cc_final: 0.7456 (mmp) REVERT: F 539 MET cc_start: 0.7465 (mtp) cc_final: 0.7230 (ttm) REVERT: F 556 MET cc_start: 0.7872 (mtp) cc_final: 0.7648 (mmt) REVERT: F 562 MET cc_start: 0.9025 (mtm) cc_final: 0.8819 (ptp) REVERT: F 638 MET cc_start: 0.7462 (mmp) cc_final: 0.7171 (mmm) REVERT: F 726 LEU cc_start: 0.6961 (mp) cc_final: 0.5996 (tt) REVERT: F 732 MET cc_start: 0.8440 (mtp) cc_final: 0.8040 (mtp) REVERT: F 853 TYR cc_start: 0.8043 (t80) cc_final: 0.7782 (t80) REVERT: F 862 MET cc_start: 0.8728 (tpp) cc_final: 0.8388 (tmm) outliers start: 0 outliers final: 0 residues processed: 722 average time/residue: 0.2157 time to fit residues: 259.2555 Evaluate side-chains 410 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS D 36 GLN D 256 GLN E 840 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065682 restraints weight = 165935.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067266 restraints weight = 98242.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068307 restraints weight = 65954.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069118 restraints weight = 49215.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069692 restraints weight = 39242.952| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40890 Z= 0.138 Angle : 0.528 6.748 55356 Z= 0.278 Chirality : 0.042 0.258 6306 Planarity : 0.004 0.068 7086 Dihedral : 5.035 53.619 5868 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.89 % 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: 1.33 (0.12), residues: 5154 helix: 2.22 (0.11), residues: 2532 sheet: 0.25 (0.19), residues: 750 loop : -0.72 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 351 TYR 0.018 0.001 TYR C 669 PHE 0.026 0.002 PHE C 721 TRP 0.009 0.001 TRP B 177 HIS 0.005 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (40890) covalent geometry : angle 0.52757 / 0.28 (55356) hydrogen bonds : bond 0.04051 / 2.80 ( 2030) hydrogen bonds : angle 3.71423 / 2.68 ( 5763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 490 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8385 (mmm) cc_final: 0.8168 (mmm) REVERT: A 578 MET cc_start: 0.8201 (tpt) cc_final: 0.7877 (tpt) REVERT: A 688 MET cc_start: 0.8909 (mmp) cc_final: 0.8489 (mtp) REVERT: A 723 ASN cc_start: 0.8478 (m-40) cc_final: 0.7791 (t0) REVERT: B 340 HIS cc_start: 0.7906 (m90) cc_final: 0.7214 (t70) REVERT: B 404 THR cc_start: 0.9174 (m) cc_final: 0.8870 (p) REVERT: B 456 ASN cc_start: 0.7678 (t0) cc_final: 0.7376 (t0) REVERT: B 457 MET cc_start: 0.5759 (mmm) cc_final: 0.5207 (tpp) REVERT: B 562 MET cc_start: 0.8677 (mtm) cc_final: 0.8184 (mtm) REVERT: B 593 MET cc_start: 0.7505 (mtp) cc_final: 0.7246 (mtp) REVERT: B 751 MET cc_start: 0.8731 (mmp) cc_final: 0.8398 (mmm) REVERT: C 484 MET cc_start: 0.7488 (mpp) cc_final: 0.7099 (mpp) REVERT: C 593 MET cc_start: 0.6700 (ttt) cc_final: 0.6279 (ttt) REVERT: C 599 PHE cc_start: 0.7600 (t80) cc_final: 0.6989 (t80) REVERT: C 633 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 638 MET cc_start: 0.7996 (mmp) cc_final: 0.7670 (mmm) REVERT: D 60 MET cc_start: 0.7926 (mtp) cc_final: 0.7689 (ttt) REVERT: D 192 GLU cc_start: 0.7738 (tp30) cc_final: 0.7504 (tp30) REVERT: D 275 ARG cc_start: 0.6669 (mmt180) cc_final: 0.5686 (mmm160) REVERT: D 581 MET cc_start: 0.8374 (pmm) cc_final: 0.7519 (ptp) REVERT: D 837 MET cc_start: 0.8530 (mmp) cc_final: 0.6335 (ttp) REVERT: E 53 MET cc_start: 0.8399 (tpt) cc_final: 0.7777 (tpp) REVERT: E 188 LEU cc_start: 0.8602 (mm) cc_final: 0.8359 (mm) REVERT: E 301 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8485 (tmmt) REVERT: E 404 THR cc_start: 0.9134 (m) cc_final: 0.8877 (p) REVERT: E 557 ASP cc_start: 0.8554 (m-30) cc_final: 0.8143 (t0) REVERT: E 581 MET cc_start: 0.7841 (mpp) cc_final: 0.7279 (mtp) REVERT: E 642 ASP cc_start: 0.8610 (t0) cc_final: 0.8325 (t0) REVERT: E 710 MET cc_start: 0.8709 (tpp) cc_final: 0.8502 (tpp) REVERT: E 856 MET cc_start: 0.8573 (mmp) cc_final: 0.8316 (mmt) REVERT: F 539 MET cc_start: 0.8147 (mtp) cc_final: 0.7813 (ttm) REVERT: F 556 MET cc_start: 0.8200 (mtp) cc_final: 0.7888 (mmt) REVERT: F 562 MET cc_start: 0.9217 (mtm) cc_final: 0.8950 (mtp) REVERT: F 581 MET cc_start: 0.7116 (mpp) cc_final: 0.6863 (mpp) REVERT: F 638 MET cc_start: 0.8027 (mmp) cc_final: 0.7597 (mmm) REVERT: F 646 MET cc_start: 0.7631 (mmp) cc_final: 0.7247 (mmm) REVERT: F 853 TYR cc_start: 0.8473 (t80) cc_final: 0.8269 (t80) outliers start: 4 outliers final: 1 residues processed: 494 average time/residue: 0.1992 time to fit residues: 168.2772 Evaluate side-chains 339 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 161 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 472 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 500 optimal weight: 8.9990 chunk 407 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 235 optimal weight: 40.0000 chunk 330 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN D 256 GLN D 748 ASN E 734 HIS F 123 ASN ** F 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 861 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059380 restraints weight = 170434.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060965 restraints weight = 97499.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062071 restraints weight = 65344.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062841 restraints weight = 48626.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063384 restraints weight = 38824.700| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40890 Z= 0.191 Angle : 0.597 7.382 55356 Z= 0.318 Chirality : 0.044 0.178 6306 Planarity : 0.004 0.062 7086 Dihedral : 5.407 59.964 5868 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 5154 helix: 1.99 (0.10), residues: 2520 sheet: 0.10 (0.20), residues: 720 loop : -0.93 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 586 TYR 0.022 0.002 TYR F 669 PHE 0.024 0.002 PHE C 721 TRP 0.013 0.001 TRP B 177 HIS 0.011 0.002 HIS F 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (40890) covalent geometry : angle 0.59676 / 0.32 (55356) hydrogen bonds : bond 0.05247 / 3.62 ( 2030) hydrogen bonds : angle 3.94026 / 2.84 ( 5763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8470 (mmm) cc_final: 0.8229 (tpp) REVERT: A 593 MET cc_start: 0.7906 (mtp) cc_final: 0.7414 (mtp) REVERT: A 688 MET cc_start: 0.9066 (mmp) cc_final: 0.8334 (mtp) REVERT: B 484 MET cc_start: 0.8544 (mpp) cc_final: 0.8301 (mpp) REVERT: B 502 TYR cc_start: 0.7915 (m-10) cc_final: 0.7686 (m-80) REVERT: B 592 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8454 (tttp) REVERT: C 19 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7593 (mmmm) REVERT: C 48 MET cc_start: 0.8791 (tmm) cc_final: 0.8369 (tmm) REVERT: C 98 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7717 (tm-30) REVERT: C 380 ASP cc_start: 0.8639 (t0) cc_final: 0.8409 (t0) REVERT: C 484 MET cc_start: 0.7448 (mpp) cc_final: 0.7243 (mpp) REVERT: C 562 MET cc_start: 0.9061 (mmm) cc_final: 0.8647 (mmm) REVERT: C 593 MET cc_start: 0.6256 (ttt) cc_final: 0.4843 (ttt) REVERT: C 599 PHE cc_start: 0.7494 (t80) cc_final: 0.6834 (t80) REVERT: C 633 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7390 (tm-30) REVERT: C 638 MET cc_start: 0.8279 (mmp) cc_final: 0.7874 (mmm) REVERT: C 688 MET cc_start: 0.8167 (tpp) cc_final: 0.7757 (tpp) REVERT: C 837 MET cc_start: 0.8599 (mmp) cc_final: 0.8381 (mmm) REVERT: D 53 MET cc_start: 0.8700 (tpp) cc_final: 0.8266 (tpp) REVERT: D 60 MET cc_start: 0.8111 (mtp) cc_final: 0.7678 (ttt) REVERT: D 86 ASN cc_start: 0.8853 (t0) cc_final: 0.8586 (t0) REVERT: D 275 ARG cc_start: 0.6702 (mmt180) cc_final: 0.6157 (tpp80) REVERT: D 478 ASP cc_start: 0.8832 (t0) cc_final: 0.8600 (t0) REVERT: D 562 MET cc_start: 0.9367 (mtm) cc_final: 0.9131 (ttp) REVERT: D 581 MET cc_start: 0.8264 (pmm) cc_final: 0.8041 (mtm) REVERT: D 627 TYR cc_start: 0.8296 (m-80) cc_final: 0.7664 (m-10) REVERT: D 672 MET cc_start: 0.8379 (tpp) cc_final: 0.8143 (tpp) REVERT: E 53 MET cc_start: 0.8582 (tpt) cc_final: 0.7839 (tpp) REVERT: E 82 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8391 (tm-30) REVERT: E 188 LEU cc_start: 0.8687 (mm) cc_final: 0.8337 (tp) REVERT: E 301 LYS cc_start: 0.8920 (mmpt) cc_final: 0.8417 (tmmt) REVERT: E 354 ASP cc_start: 0.8389 (t0) cc_final: 0.8056 (t70) REVERT: E 427 CYS cc_start: 0.8519 (m) cc_final: 0.8277 (m) REVERT: E 557 ASP cc_start: 0.8918 (m-30) cc_final: 0.8339 (t0) REVERT: E 581 MET cc_start: 0.8133 (mpp) cc_final: 0.7838 (mtt) REVERT: E 642 ASP cc_start: 0.8826 (t0) cc_final: 0.8486 (t0) REVERT: F 196 ILE cc_start: 0.8886 (mm) cc_final: 0.8679 (mm) REVERT: F 556 MET cc_start: 0.8385 (mtp) cc_final: 0.8070 (mmt) REVERT: F 581 MET cc_start: 0.7482 (mpp) cc_final: 0.7263 (mpp) REVERT: F 638 MET cc_start: 0.7864 (mmp) cc_final: 0.7460 (mmm) REVERT: F 646 MET cc_start: 0.7712 (mmp) cc_final: 0.7270 (mmm) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.2044 time to fit residues: 146.8010 Evaluate side-chains 320 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 440 optimal weight: 30.0000 chunk 113 optimal weight: 0.5980 chunk 424 optimal weight: 0.0040 chunk 142 optimal weight: 2.9990 chunk 482 optimal weight: 7.9990 chunk 433 optimal weight: 5.9990 chunk 437 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 469 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 179 optimal weight: 0.7980 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063924 restraints weight = 162589.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065473 restraints weight = 94542.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066557 restraints weight = 63661.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067272 restraints weight = 47500.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067817 restraints weight = 38196.637| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40890 Z= 0.102 Angle : 0.503 6.357 55356 Z= 0.265 Chirality : 0.042 0.146 6306 Planarity : 0.004 0.051 7086 Dihedral : 5.174 60.297 5868 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 5154 helix: 2.25 (0.11), residues: 2514 sheet: 0.12 (0.20), residues: 720 loop : -0.93 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 191 TYR 0.018 0.001 TYR A 669 PHE 0.023 0.001 PHE C 721 TRP 0.015 0.002 TRP B 430 HIS 0.005 0.001 HIS F 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (40890) covalent geometry : angle 0.50313 / 0.26 (55356) hydrogen bonds : bond 0.03696 / 2.53 ( 2030) hydrogen bonds : angle 3.59600 / 2.60 ( 5763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8331 (tpp) cc_final: 0.8098 (tpt) REVERT: A 688 MET cc_start: 0.8892 (mmp) cc_final: 0.8443 (mtp) REVERT: B 502 TYR cc_start: 0.7832 (m-10) cc_final: 0.7613 (m-80) REVERT: B 593 MET cc_start: 0.7525 (mtp) cc_final: 0.7267 (mtp) REVERT: C 48 MET cc_start: 0.8483 (tmm) cc_final: 0.8137 (tmm) REVERT: C 599 PHE cc_start: 0.7561 (t80) cc_final: 0.6942 (t80) REVERT: C 638 MET cc_start: 0.8130 (mmp) cc_final: 0.7824 (mmm) REVERT: C 688 MET cc_start: 0.8191 (tpp) cc_final: 0.7749 (tpp) REVERT: C 837 MET cc_start: 0.8706 (mmp) cc_final: 0.8477 (mmm) REVERT: D 53 MET cc_start: 0.8617 (tpp) cc_final: 0.8132 (tpp) REVERT: D 60 MET cc_start: 0.7995 (mtp) cc_final: 0.7619 (ttt) REVERT: D 190 MET cc_start: 0.8241 (mtt) cc_final: 0.7941 (mtp) REVERT: D 275 ARG cc_start: 0.6693 (mmt180) cc_final: 0.6058 (tpp80) REVERT: D 391 PHE cc_start: 0.8923 (t80) cc_final: 0.8639 (t80) REVERT: D 571 VAL cc_start: 0.8907 (t) cc_final: 0.8682 (t) REVERT: D 627 TYR cc_start: 0.8059 (m-80) cc_final: 0.7724 (m-10) REVERT: E 53 MET cc_start: 0.8362 (tpt) cc_final: 0.7738 (tpp) REVERT: E 354 ASP cc_start: 0.8404 (t0) cc_final: 0.8160 (t70) REVERT: E 427 CYS cc_start: 0.8507 (m) cc_final: 0.8259 (m) REVERT: E 538 GLU cc_start: 0.8492 (pp20) cc_final: 0.8287 (pp20) REVERT: E 557 ASP cc_start: 0.8696 (m-30) cc_final: 0.8094 (t70) REVERT: E 581 MET cc_start: 0.7875 (mpp) cc_final: 0.7309 (mtp) REVERT: E 642 ASP cc_start: 0.8556 (t0) cc_final: 0.8313 (t0) REVERT: F 484 MET cc_start: 0.7248 (mpp) cc_final: 0.7042 (mpp) REVERT: F 556 MET cc_start: 0.8417 (mtp) cc_final: 0.8109 (mmt) REVERT: F 646 MET cc_start: 0.7778 (mmp) cc_final: 0.7365 (mmm) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.2069 time to fit residues: 153.5485 Evaluate side-chains 333 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 chunk 311 optimal weight: 2.9990 chunk 241 optimal weight: 0.0470 chunk 351 optimal weight: 3.9990 chunk 399 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN D 78 HIS D 759 ASN ** F 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060772 restraints weight = 162645.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062254 restraints weight = 95378.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063308 restraints weight = 64498.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063983 restraints weight = 48370.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064510 restraints weight = 39207.750| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40890 Z= 0.167 Angle : 0.573 8.896 55356 Z= 0.303 Chirality : 0.043 0.148 6306 Planarity : 0.004 0.055 7086 Dihedral : 5.412 63.415 5868 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % 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: 0.95 (0.12), residues: 5154 helix: 2.02 (0.10), residues: 2520 sheet: 0.16 (0.20), residues: 648 loop : -1.07 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 191 TYR 0.029 0.001 TYR B 863 PHE 0.023 0.002 PHE F 44 TRP 0.012 0.002 TRP C 563 HIS 0.007 0.001 HIS F 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (40890) covalent geometry : angle 0.57320 / 0.30 (55356) hydrogen bonds : bond 0.04836 / 3.34 ( 2030) hydrogen bonds : angle 3.82973 / 2.76 ( 5763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.7705 (mtp) cc_final: 0.7395 (mtp) REVERT: A 629 LEU cc_start: 0.8869 (pp) cc_final: 0.8656 (pp) REVERT: A 688 MET cc_start: 0.8967 (mmp) cc_final: 0.8293 (mtp) REVERT: B 562 MET cc_start: 0.8745 (mtm) cc_final: 0.8404 (mtm) REVERT: B 592 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8346 (tttp) REVERT: C 10 VAL cc_start: 0.8279 (t) cc_final: 0.7945 (t) REVERT: C 48 MET cc_start: 0.8522 (tmm) cc_final: 0.8207 (tmm) REVERT: C 484 MET cc_start: 0.7536 (mpp) cc_final: 0.7209 (mpp) REVERT: C 562 MET cc_start: 0.9216 (mmt) cc_final: 0.8755 (mmm) REVERT: C 593 MET cc_start: 0.5938 (ttt) cc_final: 0.5672 (tmm) REVERT: C 599 PHE cc_start: 0.7476 (t80) cc_final: 0.6814 (t80) REVERT: C 638 MET cc_start: 0.8208 (mmp) cc_final: 0.7897 (mmm) REVERT: C 688 MET cc_start: 0.8203 (tpp) cc_final: 0.7745 (tpp) REVERT: C 837 MET cc_start: 0.8769 (mmp) cc_final: 0.8560 (mmm) REVERT: D 53 MET cc_start: 0.8787 (tpp) cc_final: 0.8265 (tpp) REVERT: D 60 MET cc_start: 0.8015 (mtp) cc_final: 0.7637 (ttt) REVERT: D 275 ARG cc_start: 0.6802 (mmt180) cc_final: 0.6209 (tpp80) REVERT: D 349 MET cc_start: 0.8550 (tmm) cc_final: 0.7706 (tmm) REVERT: D 383 THR cc_start: 0.8586 (p) cc_final: 0.8365 (p) REVERT: D 571 VAL cc_start: 0.9018 (t) cc_final: 0.8725 (t) REVERT: D 581 MET cc_start: 0.8342 (pmm) cc_final: 0.7437 (ptp) REVERT: E 53 MET cc_start: 0.8355 (tpt) cc_final: 0.7934 (tpp) REVERT: E 250 MET cc_start: 0.7963 (ptp) cc_final: 0.7756 (ptp) REVERT: E 354 ASP cc_start: 0.8455 (t0) cc_final: 0.8218 (t70) REVERT: E 427 CYS cc_start: 0.8496 (m) cc_final: 0.8266 (m) REVERT: E 437 ASP cc_start: 0.7658 (m-30) cc_final: 0.7431 (m-30) REVERT: E 557 ASP cc_start: 0.8742 (m-30) cc_final: 0.8284 (t70) REVERT: E 581 MET cc_start: 0.8028 (mpp) cc_final: 0.7602 (mtp) REVERT: E 642 ASP cc_start: 0.8733 (t0) cc_final: 0.8394 (t0) REVERT: E 856 MET cc_start: 0.8596 (mmp) cc_final: 0.8388 (mmt) REVERT: F 556 MET cc_start: 0.8502 (mtp) cc_final: 0.7815 (mmt) REVERT: F 638 MET cc_start: 0.7943 (mmp) cc_final: 0.7450 (mmm) outliers start: 2 outliers final: 0 residues processed: 403 average time/residue: 0.2111 time to fit residues: 146.9908 Evaluate side-chains 316 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 384 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 278 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 410 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 340 HIS ** F 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060644 restraints weight = 169138.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062279 restraints weight = 95498.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063364 restraints weight = 63455.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064122 restraints weight = 47259.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064720 restraints weight = 37887.344| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40890 Z= 0.110 Angle : 0.522 8.722 55356 Z= 0.271 Chirality : 0.042 0.156 6306 Planarity : 0.004 0.053 7086 Dihedral : 5.275 63.671 5868 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.08 (0.12), residues: 5154 helix: 2.17 (0.11), residues: 2520 sheet: 0.19 (0.20), residues: 648 loop : -1.05 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 191 TYR 0.020 0.001 TYR E 669 PHE 0.021 0.001 PHE D 721 TRP 0.009 0.001 TRP A 459 HIS 0.010 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (40890) covalent geometry : angle 0.52203 / 0.27 (55356) hydrogen bonds : bond 0.03873 / 2.66 ( 2030) hydrogen bonds : angle 3.63915 / 2.63 ( 5763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.7961 (mtp) cc_final: 0.7649 (mtp) REVERT: A 688 MET cc_start: 0.9052 (mmp) cc_final: 0.8388 (mtp) REVERT: B 478 ASP cc_start: 0.8771 (t70) cc_final: 0.8568 (t0) REVERT: B 484 MET cc_start: 0.8537 (mpp) cc_final: 0.8288 (mpp) REVERT: B 592 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8410 (tttp) REVERT: B 593 MET cc_start: 0.7769 (mtp) cc_final: 0.7448 (mtp) REVERT: B 708 GLU cc_start: 0.8853 (pp20) cc_final: 0.8430 (pt0) REVERT: C 48 MET cc_start: 0.8809 (tmm) cc_final: 0.8411 (tmm) REVERT: C 484 MET cc_start: 0.7446 (mpp) cc_final: 0.6892 (mpp) REVERT: C 562 MET cc_start: 0.9148 (mmt) cc_final: 0.8816 (mmm) REVERT: C 599 PHE cc_start: 0.7327 (t80) cc_final: 0.6654 (t80) REVERT: C 638 MET cc_start: 0.8363 (mmp) cc_final: 0.7964 (mmm) REVERT: C 645 MET cc_start: 0.8088 (mpp) cc_final: 0.7874 (mpp) REVERT: C 688 MET cc_start: 0.8090 (tpp) cc_final: 0.7635 (tpp) REVERT: C 837 MET cc_start: 0.8678 (mmp) cc_final: 0.8347 (mmm) REVERT: D 53 MET cc_start: 0.8944 (tpp) cc_final: 0.8302 (tpp) REVERT: D 60 MET cc_start: 0.8075 (mtp) cc_final: 0.7604 (ttt) REVERT: D 275 ARG cc_start: 0.6710 (mmt180) cc_final: 0.6074 (tpp80) REVERT: D 383 THR cc_start: 0.8710 (p) cc_final: 0.8509 (p) REVERT: D 571 VAL cc_start: 0.9006 (t) cc_final: 0.8805 (t) REVERT: D 581 MET cc_start: 0.8225 (pmm) cc_final: 0.7952 (ptp) REVERT: D 627 TYR cc_start: 0.8257 (m-80) cc_final: 0.7696 (m-10) REVERT: E 301 LYS cc_start: 0.8930 (mmpt) cc_final: 0.8617 (pptt) REVERT: E 354 ASP cc_start: 0.8423 (t0) cc_final: 0.8080 (t70) REVERT: E 427 CYS cc_start: 0.8662 (m) cc_final: 0.8397 (m) REVERT: E 437 ASP cc_start: 0.7962 (m-30) cc_final: 0.7736 (m-30) REVERT: E 557 ASP cc_start: 0.8890 (m-30) cc_final: 0.8267 (t70) REVERT: E 565 MET cc_start: 0.8663 (ttp) cc_final: 0.8433 (ttt) REVERT: E 581 MET cc_start: 0.8117 (mpp) cc_final: 0.7673 (mtp) REVERT: E 642 ASP cc_start: 0.8655 (t0) cc_final: 0.8405 (t0) REVERT: F 556 MET cc_start: 0.8470 (mtp) cc_final: 0.7781 (mmt) REVERT: F 638 MET cc_start: 0.7821 (mmp) cc_final: 0.7388 (mmm) REVERT: F 646 MET cc_start: 0.8173 (mmp) cc_final: 0.7723 (mmm) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2109 time to fit residues: 149.8686 Evaluate side-chains 320 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 348 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 373 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 412 optimal weight: 0.5980 chunk 514 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.076384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061255 restraints weight = 164165.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062756 restraints weight = 95489.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063829 restraints weight = 64420.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064495 restraints weight = 48060.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065033 restraints weight = 38971.835| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40890 Z= 0.144 Angle : 0.548 7.626 55356 Z= 0.288 Chirality : 0.043 0.155 6306 Planarity : 0.004 0.053 7086 Dihedral : 5.358 65.046 5868 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 5154 helix: 2.08 (0.11), residues: 2520 sheet: 0.12 (0.20), residues: 648 loop : -1.09 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 586 TYR 0.020 0.001 TYR F 669 PHE 0.036 0.002 PHE E 391 TRP 0.018 0.001 TRP D 430 HIS 0.005 0.001 HIS E 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (40890) covalent geometry : angle 0.54850 / 0.29 (55356) hydrogen bonds : bond 0.04306 / 2.97 ( 2030) hydrogen bonds : angle 3.73970 / 2.70 ( 5763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.7756 (mtp) cc_final: 0.7443 (mtp) REVERT: A 688 MET cc_start: 0.8935 (mmp) cc_final: 0.8229 (mtp) REVERT: B 592 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8325 (tttp) REVERT: B 593 MET cc_start: 0.7605 (mtp) cc_final: 0.7392 (mtp) REVERT: B 708 GLU cc_start: 0.8719 (pp20) cc_final: 0.8422 (tm-30) REVERT: C 48 MET cc_start: 0.8505 (tmm) cc_final: 0.8230 (tmm) REVERT: C 481 LYS cc_start: 0.8249 (pttt) cc_final: 0.7892 (pttp) REVERT: C 484 MET cc_start: 0.7633 (mpp) cc_final: 0.7186 (mpp) REVERT: C 562 MET cc_start: 0.9153 (mmt) cc_final: 0.8828 (mmm) REVERT: C 593 MET cc_start: 0.6578 (tmm) cc_final: 0.6130 (tmm) REVERT: C 599 PHE cc_start: 0.7329 (t80) cc_final: 0.6766 (t80) REVERT: C 638 MET cc_start: 0.8259 (mmp) cc_final: 0.7946 (mmm) REVERT: C 688 MET cc_start: 0.8181 (tpp) cc_final: 0.7710 (tpp) REVERT: C 837 MET cc_start: 0.8768 (mmp) cc_final: 0.8557 (mmm) REVERT: D 53 MET cc_start: 0.8858 (tpp) cc_final: 0.8349 (tpp) REVERT: D 60 MET cc_start: 0.8025 (mtp) cc_final: 0.7662 (ttt) REVERT: D 275 ARG cc_start: 0.6711 (mmt180) cc_final: 0.6097 (tpp80) REVERT: D 383 THR cc_start: 0.8621 (p) cc_final: 0.8395 (p) REVERT: D 571 VAL cc_start: 0.9022 (t) cc_final: 0.8819 (t) REVERT: D 581 MET cc_start: 0.8180 (pmm) cc_final: 0.7625 (ptp) REVERT: E 301 LYS cc_start: 0.8841 (mmpt) cc_final: 0.8587 (pptt) REVERT: E 349 MET cc_start: 0.8725 (ttp) cc_final: 0.8422 (ttt) REVERT: E 557 ASP cc_start: 0.8725 (m-30) cc_final: 0.8255 (t70) REVERT: E 565 MET cc_start: 0.8523 (ttp) cc_final: 0.8317 (ttt) REVERT: E 581 MET cc_start: 0.7993 (mpp) cc_final: 0.7516 (mtp) REVERT: E 642 ASP cc_start: 0.8688 (t0) cc_final: 0.8363 (t0) REVERT: E 710 MET cc_start: 0.8953 (tpp) cc_final: 0.8722 (tpp) REVERT: E 751 MET cc_start: 0.9066 (mmp) cc_final: 0.8756 (mmp) REVERT: F 196 ILE cc_start: 0.8691 (mm) cc_final: 0.8421 (mm) REVERT: F 638 MET cc_start: 0.7999 (mmp) cc_final: 0.7558 (mmm) REVERT: F 646 MET cc_start: 0.8244 (mmp) cc_final: 0.7730 (mmm) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.2062 time to fit residues: 140.5919 Evaluate side-chains 315 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 293 optimal weight: 7.9990 chunk 488 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 386 optimal weight: 0.8980 chunk 417 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 487 optimal weight: 0.0970 chunk 372 optimal weight: 0.0270 chunk 182 optimal weight: 5.9990 chunk 415 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 overall best weight: 2.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.059808 restraints weight = 168432.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061404 restraints weight = 95248.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062521 restraints weight = 63603.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063291 restraints weight = 46929.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063809 restraints weight = 37545.683| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40890 Z= 0.131 Angle : 0.551 11.694 55356 Z= 0.287 Chirality : 0.043 0.146 6306 Planarity : 0.004 0.054 7086 Dihedral : 5.375 65.958 5868 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.97 (0.12), residues: 5154 helix: 2.11 (0.11), residues: 2514 sheet: 0.09 (0.20), residues: 648 loop : -1.12 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 586 TYR 0.025 0.001 TYR A 863 PHE 0.036 0.002 PHE D 391 TRP 0.011 0.001 TRP C 563 HIS 0.010 0.001 HIS F 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (40890) covalent geometry : angle 0.55148 / 0.29 (55356) hydrogen bonds : bond 0.04156 / 2.86 ( 2030) hydrogen bonds : angle 3.74285 / 2.71 ( 5763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.9115 (pt) cc_final: 0.8764 (mm) REVERT: A 593 MET cc_start: 0.8135 (mtp) cc_final: 0.7735 (mtp) REVERT: B 478 ASP cc_start: 0.8822 (t70) cc_final: 0.8596 (t0) REVERT: B 578 MET cc_start: 0.7915 (mmm) cc_final: 0.7384 (mpp) REVERT: B 592 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8406 (tttp) REVERT: B 679 ASP cc_start: 0.8617 (p0) cc_final: 0.8408 (p0) REVERT: B 708 GLU cc_start: 0.8887 (pp20) cc_final: 0.8625 (tm-30) REVERT: C 48 MET cc_start: 0.8812 (tmm) cc_final: 0.8457 (tmm) REVERT: C 349 MET cc_start: 0.8919 (tmm) cc_final: 0.8608 (tmm) REVERT: C 481 LYS cc_start: 0.8184 (pttt) cc_final: 0.7822 (pttp) REVERT: C 484 MET cc_start: 0.7601 (mpp) cc_final: 0.7135 (mpp) REVERT: C 593 MET cc_start: 0.6397 (tmm) cc_final: 0.5979 (tmm) REVERT: C 599 PHE cc_start: 0.7181 (t80) cc_final: 0.6563 (t80) REVERT: C 638 MET cc_start: 0.8390 (mmp) cc_final: 0.8027 (mmm) REVERT: C 645 MET cc_start: 0.8122 (mpp) cc_final: 0.7904 (mpp) REVERT: C 688 MET cc_start: 0.8090 (tpp) cc_final: 0.7636 (tpp) REVERT: D 53 MET cc_start: 0.9052 (tpp) cc_final: 0.8447 (tpp) REVERT: D 60 MET cc_start: 0.8094 (mtp) cc_final: 0.7636 (ttt) REVERT: D 349 MET cc_start: 0.8459 (tmm) cc_final: 0.7428 (tmm) REVERT: D 383 THR cc_start: 0.8766 (p) cc_final: 0.8553 (p) REVERT: E 301 LYS cc_start: 0.8945 (mmpt) cc_final: 0.8591 (pptt) REVERT: E 349 MET cc_start: 0.8930 (ttp) cc_final: 0.8576 (ttt) REVERT: E 354 ASP cc_start: 0.8235 (t0) cc_final: 0.7853 (t70) REVERT: E 427 CYS cc_start: 0.8571 (m) cc_final: 0.8349 (m) REVERT: E 557 ASP cc_start: 0.8913 (m-30) cc_final: 0.8357 (t70) REVERT: E 581 MET cc_start: 0.8214 (mpp) cc_final: 0.7799 (mtp) REVERT: E 642 ASP cc_start: 0.8746 (t0) cc_final: 0.8433 (t0) REVERT: E 710 MET cc_start: 0.8917 (tpp) cc_final: 0.8693 (tpp) REVERT: F 190 MET cc_start: 0.8470 (mtm) cc_final: 0.8270 (mtm) REVERT: F 196 ILE cc_start: 0.8774 (mm) cc_final: 0.8500 (mm) REVERT: F 638 MET cc_start: 0.7824 (mmp) cc_final: 0.7390 (mmm) REVERT: F 646 MET cc_start: 0.8290 (mmp) cc_final: 0.7789 (mmm) REVERT: F 862 MET cc_start: 0.8932 (tmm) cc_final: 0.8689 (tmm) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.2167 time to fit residues: 148.5036 Evaluate side-chains 320 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 95 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 444 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS E 373 HIS F 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058038 restraints weight = 170935.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059617 restraints weight = 95876.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060691 restraints weight = 63707.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061488 restraints weight = 47273.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062050 restraints weight = 37502.620| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40890 Z= 0.178 Angle : 0.609 11.014 55356 Z= 0.320 Chirality : 0.044 0.164 6306 Planarity : 0.004 0.059 7086 Dihedral : 5.629 68.118 5868 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.74 (0.12), residues: 5154 helix: 1.90 (0.11), residues: 2520 sheet: 0.01 (0.20), residues: 678 loop : -1.24 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 54 TYR 0.027 0.001 TYR A 863 PHE 0.031 0.002 PHE D 391 TRP 0.015 0.001 TRP C 563 HIS 0.011 0.001 HIS F 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (40890) covalent geometry : angle 0.60882 / 0.32 (55356) hydrogen bonds : bond 0.05026 / 3.46 ( 2030) hydrogen bonds : angle 4.01429 / 2.90 ( 5763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.616 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 67 MET cc_start: 0.8170 (tmm) cc_final: 0.7217 (tmm) REVERT: A 468 ILE cc_start: 0.9217 (pt) cc_final: 0.8840 (mm) REVERT: A 469 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7469 (mmtt) REVERT: A 593 MET cc_start: 0.8144 (mtp) cc_final: 0.7767 (mtp) REVERT: A 688 MET cc_start: 0.9042 (mmp) cc_final: 0.8285 (mtp) REVERT: B 592 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8486 (tttp) REVERT: B 679 ASP cc_start: 0.8697 (p0) cc_final: 0.8490 (p0) REVERT: B 708 GLU cc_start: 0.8919 (pp20) cc_final: 0.8685 (tm-30) REVERT: C 48 MET cc_start: 0.8925 (tmm) cc_final: 0.8539 (tmm) REVERT: C 457 MET cc_start: 0.8369 (mmp) cc_final: 0.7805 (tpp) REVERT: C 484 MET cc_start: 0.7634 (mpp) cc_final: 0.7185 (mpp) REVERT: C 599 PHE cc_start: 0.7114 (t80) cc_final: 0.6453 (t80) REVERT: C 638 MET cc_start: 0.8477 (mmp) cc_final: 0.8116 (mmm) REVERT: C 645 MET cc_start: 0.8110 (mpp) cc_final: 0.7893 (mpp) REVERT: C 688 MET cc_start: 0.8097 (tpp) cc_final: 0.7647 (tpp) REVERT: D 53 MET cc_start: 0.9114 (tpp) cc_final: 0.8516 (tpp) REVERT: D 60 MET cc_start: 0.8108 (mtp) cc_final: 0.7624 (ttt) REVERT: D 67 MET cc_start: 0.6639 (tmm) cc_final: 0.6226 (tmm) REVERT: D 349 MET cc_start: 0.8432 (tmm) cc_final: 0.7587 (tmm) REVERT: D 571 VAL cc_start: 0.9092 (t) cc_final: 0.8784 (t) REVERT: D 576 MET cc_start: 0.8590 (mtm) cc_final: 0.8356 (mtm) REVERT: D 679 ASP cc_start: 0.7867 (p0) cc_final: 0.6714 (m-30) REVERT: E 53 MET cc_start: 0.8470 (tpp) cc_final: 0.8180 (tpp) REVERT: E 301 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8628 (pptt) REVERT: E 349 MET cc_start: 0.8972 (ttp) cc_final: 0.8619 (ttp) REVERT: E 354 ASP cc_start: 0.8288 (t0) cc_final: 0.7894 (t70) REVERT: E 457 MET cc_start: 0.7015 (tpp) cc_final: 0.6702 (tpp) REVERT: E 557 ASP cc_start: 0.8927 (m-30) cc_final: 0.8425 (t70) REVERT: E 581 MET cc_start: 0.8293 (mpp) cc_final: 0.7738 (mtt) REVERT: E 642 ASP cc_start: 0.8737 (t0) cc_final: 0.8403 (t0) REVERT: E 710 MET cc_start: 0.8954 (tpp) cc_final: 0.8740 (tpp) REVERT: F 196 ILE cc_start: 0.8822 (mm) cc_final: 0.8549 (mm) REVERT: F 638 MET cc_start: 0.7721 (mmp) cc_final: 0.7300 (mmm) REVERT: F 646 MET cc_start: 0.8449 (mmp) cc_final: 0.7841 (mmm) REVERT: F 862 MET cc_start: 0.8925 (tmm) cc_final: 0.8715 (tmm) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2182 time to fit residues: 146.5136 Evaluate side-chains 315 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 274 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 464 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058734 restraints weight = 167486.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060307 restraints weight = 94665.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061410 restraints weight = 62666.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062126 restraints weight = 46432.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062704 restraints weight = 37375.867| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40890 Z= 0.150 Angle : 0.587 8.539 55356 Z= 0.306 Chirality : 0.043 0.142 6306 Planarity : 0.004 0.059 7086 Dihedral : 5.603 68.824 5868 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 5154 helix: 1.94 (0.10), residues: 2520 sheet: -0.05 (0.20), residues: 678 loop : -1.27 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 584 TYR 0.025 0.001 TYR A 863 PHE 0.024 0.002 PHE B 690 TRP 0.011 0.001 TRP A 459 HIS 0.009 0.001 HIS F 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (40890) covalent geometry : angle 0.58725 / 0.31 (55356) hydrogen bonds : bond 0.04578 / 3.15 ( 2030) hydrogen bonds : angle 3.91816 / 2.83 ( 5763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.275 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: A 67 MET cc_start: 0.8183 (tmm) cc_final: 0.7703 (tmm) REVERT: A 468 ILE cc_start: 0.9169 (pt) cc_final: 0.8779 (mm) REVERT: A 513 MET cc_start: 0.7663 (mmm) cc_final: 0.7426 (mtp) REVERT: A 593 MET cc_start: 0.8135 (mtp) cc_final: 0.7723 (mtp) REVERT: A 688 MET cc_start: 0.9006 (mmp) cc_final: 0.8293 (mtp) REVERT: B 562 MET cc_start: 0.9045 (mtm) cc_final: 0.8278 (mtm) REVERT: B 578 MET cc_start: 0.7935 (mmm) cc_final: 0.7464 (mpp) REVERT: B 592 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8440 (tttp) REVERT: B 679 ASP cc_start: 0.8595 (p0) cc_final: 0.8380 (p0) REVERT: B 708 GLU cc_start: 0.8882 (pp20) cc_final: 0.8629 (tm-30) REVERT: C 48 MET cc_start: 0.8861 (tmm) cc_final: 0.8497 (tmm) REVERT: C 457 MET cc_start: 0.8344 (mmp) cc_final: 0.7836 (tpp) REVERT: C 484 MET cc_start: 0.7729 (mpp) cc_final: 0.7326 (mpp) REVERT: C 599 PHE cc_start: 0.7127 (t80) cc_final: 0.6442 (t80) REVERT: C 638 MET cc_start: 0.8463 (mmp) cc_final: 0.8114 (mmm) REVERT: C 645 MET cc_start: 0.8115 (mpp) cc_final: 0.7913 (mpp) REVERT: C 688 MET cc_start: 0.8110 (tpp) cc_final: 0.7649 (tpp) REVERT: D 60 MET cc_start: 0.8082 (mtp) cc_final: 0.7615 (ttt) REVERT: D 67 MET cc_start: 0.6659 (tmm) cc_final: 0.6232 (tmm) REVERT: D 229 ASP cc_start: 0.7503 (p0) cc_final: 0.6824 (t0) REVERT: D 468 ILE cc_start: 0.8434 (pt) cc_final: 0.8000 (mm) REVERT: D 478 ASP cc_start: 0.8769 (t0) cc_final: 0.8566 (t0) REVERT: D 679 ASP cc_start: 0.7862 (p0) cc_final: 0.6639 (m-30) REVERT: E 53 MET cc_start: 0.8429 (tpp) cc_final: 0.8135 (tpp) REVERT: E 301 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8603 (pptt) REVERT: E 349 MET cc_start: 0.8910 (ttp) cc_final: 0.8578 (ttp) REVERT: E 354 ASP cc_start: 0.8307 (t0) cc_final: 0.7950 (t70) REVERT: E 457 MET cc_start: 0.7048 (tpp) cc_final: 0.6737 (tpp) REVERT: E 557 ASP cc_start: 0.8902 (m-30) cc_final: 0.8368 (t70) REVERT: E 581 MET cc_start: 0.8243 (mpp) cc_final: 0.7821 (mtp) REVERT: E 642 ASP cc_start: 0.8729 (t0) cc_final: 0.8382 (t0) REVERT: E 710 MET cc_start: 0.8969 (tpp) cc_final: 0.8739 (tpp) REVERT: E 767 MET cc_start: 0.8328 (mmm) cc_final: 0.8043 (tpp) REVERT: F 565 MET cc_start: 0.8891 (ttm) cc_final: 0.8587 (mmm) REVERT: F 638 MET cc_start: 0.7815 (mmp) cc_final: 0.7385 (mmm) REVERT: F 646 MET cc_start: 0.8448 (mmp) cc_final: 0.7814 (mmm) REVERT: F 862 MET cc_start: 0.8936 (tmm) cc_final: 0.8725 (tmm) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1968 time to fit residues: 128.0975 Evaluate side-chains 313 residues out of total 4236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 81 optimal weight: 7.9990 chunk 481 optimal weight: 4.9990 chunk 418 optimal weight: 0.6980 chunk 273 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 465 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 461 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 HIS ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.058812 restraints weight = 169520.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.060417 restraints weight = 94599.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061543 restraints weight = 62518.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062301 restraints weight = 45964.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062811 restraints weight = 36691.672| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40890 Z= 0.141 Angle : 0.577 8.605 55356 Z= 0.301 Chirality : 0.043 0.144 6306 Planarity : 0.004 0.059 7086 Dihedral : 5.581 69.316 5868 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.74 (0.12), residues: 5154 helix: 1.95 (0.11), residues: 2520 sheet: -0.07 (0.20), residues: 678 loop : -1.28 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 586 TYR 0.024 0.001 TYR A 863 PHE 0.023 0.002 PHE B 690 TRP 0.016 0.001 TRP C 563 HIS 0.008 0.001 HIS F 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (40890) covalent geometry : angle 0.57666 / 0.30 (55356) hydrogen bonds : bond 0.04436 / 3.05 ( 2030) hydrogen bonds : angle 3.89467 / 2.82 ( 5763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7145.60 seconds wall clock time: 123 minutes 58.65 seconds (7438.65 seconds total)