Starting phenix.real_space_refine on Sat Mar 7 15:26:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dag_30625/03_2026/7dag_30625.map" } resolution = 4.37 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= 0.007 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 203 5.16 5 C 29218 2.51 5 N 7833 2.21 5 O 8722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "B" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "C" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "D" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "E" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "F" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "G" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3250 Classifications: {'peptide': 419} Link IDs: {'CIS': 5, 'PTRANS': 21, 'TRANS': 392} Chain: "H" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3318 Classifications: {'peptide': 448} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 429} Time building chain proxies: 10.43, per 1000 atoms: 0.23 Number of scatterers: 45976 At special positions: 0 Unit cell: (169.148, 192.449, 174.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 203 16.00 O 8722 8.00 N 7833 7.00 C 29218 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: 4.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11256 Finding SS restraints... Secondary structure from input PDB file: 231 helices and 30 sheets defined 49.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 195 through 204 removed outlier: 3.512A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL A 244 " --> pdb=" O ASP A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.301A pdb=" N ILE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 644 through 663 Processing helix chain 'A' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP A 671 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN A 673 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 697 through 713 Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.761A pdb=" N SER A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.981A pdb=" N LEU B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.701A pdb=" N LYS B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 4.002A pdb=" N ALA B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 removed outlier: 3.525A pdb=" N VAL B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 365 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 435 through 438 Processing helix chain 'B' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL B 498 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 644 through 663 Processing helix chain 'B' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP B 671 " --> pdb=" O ASN B 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) Proline residue: B 686 - end of helix Processing helix chain 'B' and resid 697 through 713 Processing helix chain 'B' and resid 719 through 733 removed outlier: 3.763A pdb=" N SER B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 742 Processing helix chain 'B' and resid 743 through 752 Processing helix chain 'B' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 27 through 45 removed outlier: 4.801A pdb=" N LYS C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.703A pdb=" N LYS C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 4.004A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.525A pdb=" N VAL C 244 " --> pdb=" O ASP C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 307 Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.982A pdb=" N ILE C 363 " --> pdb=" O THR C 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 365 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'C' and resid 435 through 438 Processing helix chain 'C' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL C 498 " --> pdb=" O TYR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 624 through 627 Processing helix chain 'C' and resid 644 through 663 Processing helix chain 'C' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP C 671 " --> pdb=" O ASN C 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU C 683 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR C 684 " --> pdb=" O MET C 680 " (cutoff:3.500A) Proline residue: C 686 - end of helix Processing helix chain 'C' and resid 697 through 713 Processing helix chain 'C' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER C 723 " --> pdb=" O GLY C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 742 Processing helix chain 'C' and resid 743 through 752 Processing helix chain 'C' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 837 " --> pdb=" O VAL C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL D 244 " --> pdb=" O ASP D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 241 through 244' Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 365 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 435 through 438 Processing helix chain 'D' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL D 498 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 560 removed outlier: 3.851A pdb=" N ASP D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 624 through 627 Processing helix chain 'D' and resid 644 through 663 Processing helix chain 'D' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP D 671 " --> pdb=" O ASN D 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 672 " --> pdb=" O GLU D 668 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN D 673 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU D 683 " --> pdb=" O LYS D 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D 684 " --> pdb=" O MET D 680 " (cutoff:3.500A) Proline residue: D 686 - end of helix Processing helix chain 'D' and resid 697 through 713 Processing helix chain 'D' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER D 723 " --> pdb=" O GLY D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 742 Processing helix chain 'D' and resid 743 through 752 Processing helix chain 'D' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 808 removed outlier: 3.668A pdb=" N LEU D 808 " --> pdb=" O LEU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU D 830 " --> pdb=" O ALA D 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 837 " --> pdb=" O VAL D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU D 853 " --> pdb=" O LEU D 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 80 removed outlier: 3.703A pdb=" N LYS E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 143 through 159 Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 244' Processing helix chain 'E' and resid 258 through 268 Processing helix chain 'E' and resid 277 through 287 removed outlier: 4.886A pdb=" N VAL E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'E' and resid 349 through 365 removed outlier: 3.982A pdb=" N ILE E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY E 364 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 435 through 438 Processing helix chain 'E' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE E 470 " --> pdb=" O GLY E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 492 Processing helix chain 'E' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL E 498 " --> pdb=" O TYR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS E 526 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP E 549 " --> pdb=" O GLY E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 624 through 627 Processing helix chain 'E' and resid 644 through 663 Processing helix chain 'E' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP E 671 " --> pdb=" O ASN E 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY E 672 " --> pdb=" O GLU E 668 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN E 673 " --> pdb=" O TYR E 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 682 " --> pdb=" O LEU E 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU E 683 " --> pdb=" O LYS E 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR E 684 " --> pdb=" O MET E 680 " (cutoff:3.500A) Proline residue: E 686 - end of helix Processing helix chain 'E' and resid 697 through 713 Processing helix chain 'E' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER E 723 " --> pdb=" O GLY E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 742 Processing helix chain 'E' and resid 743 through 752 Processing helix chain 'E' and resid 769 through 781 removed outlier: 3.558A pdb=" N ARG E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 808 removed outlier: 3.668A pdb=" N LEU E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP E 829 " --> pdb=" O LEU E 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU E 830 " --> pdb=" O ALA E 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU E 853 " --> pdb=" O LEU E 849 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 24 Processing helix chain 'F' and resid 27 through 45 removed outlier: 4.801A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'F' and resid 174 through 183 Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.512A pdb=" N ALA F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 240 removed outlier: 4.004A pdb=" N ALA F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL F 244 " --> pdb=" O ASP F 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 241 through 244' Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 277 through 287 removed outlier: 4.886A pdb=" N VAL F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 307 Processing helix chain 'F' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE F 363 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY F 364 " --> pdb=" O MET F 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 365 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 435 through 438 Processing helix chain 'F' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE F 470 " --> pdb=" O GLY F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 492 Processing helix chain 'F' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL F 498 " --> pdb=" O TYR F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS F 526 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP F 549 " --> pdb=" O GLY F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 Processing helix chain 'F' and resid 624 through 627 Processing helix chain 'F' and resid 644 through 663 Processing helix chain 'F' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP F 671 " --> pdb=" O ASN F 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY F 672 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN F 673 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU F 683 " --> pdb=" O LYS F 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR F 684 " --> pdb=" O MET F 680 " (cutoff:3.500A) Proline residue: F 686 - end of helix Processing helix chain 'F' and resid 697 through 713 Processing helix chain 'F' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER F 723 " --> pdb=" O GLY F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 742 Processing helix chain 'F' and resid 743 through 752 Processing helix chain 'F' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG F 773 " --> pdb=" O GLN F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP F 829 " --> pdb=" O LEU F 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU F 830 " --> pdb=" O ALA F 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP F 837 " --> pdb=" O VAL F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 862 removed outlier: 3.528A pdb=" N LEU F 853 " --> pdb=" O LEU F 849 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 474 removed outlier: 4.543A pdb=" N ASP G 474 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 492 Processing helix chain 'G' and resid 494 through 506 removed outlier: 3.523A pdb=" N VAL G 498 " --> pdb=" O TYR G 494 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN G 505 " --> pdb=" O LEU G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 535 Processing helix chain 'G' and resid 545 through 560 Processing helix chain 'G' and resid 564 through 572 removed outlier: 4.014A pdb=" N LEU G 568 " --> pdb=" O HIS G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 627 Processing helix chain 'G' and resid 644 through 662 removed outlier: 3.705A pdb=" N VAL G 662 " --> pdb=" O LEU G 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 691 removed outlier: 4.151A pdb=" N ASP G 671 " --> pdb=" O ASN G 667 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY G 672 " --> pdb=" O GLU G 668 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN G 673 " --> pdb=" O TYR G 669 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 682 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU G 683 " --> pdb=" O LYS G 679 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR G 684 " --> pdb=" O MET G 680 " (cutoff:3.500A) Proline residue: G 686 - end of helix Processing helix chain 'G' and resid 697 through 714 Processing helix chain 'G' and resid 719 through 733 removed outlier: 3.595A pdb=" N SER G 723 " --> pdb=" O GLY G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 743 through 752 Processing helix chain 'G' and resid 769 through 781 Processing helix chain 'G' and resid 789 through 808 Processing helix chain 'G' and resid 820 through 837 removed outlier: 4.434A pdb=" N ASP G 829 " --> pdb=" O LEU G 825 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU G 830 " --> pdb=" O ALA G 826 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP G 837 " --> pdb=" O VAL G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 863 removed outlier: 3.613A pdb=" N LEU G 853 " --> pdb=" O LEU G 849 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS G 854 " --> pdb=" O ILE G 850 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 855 " --> pdb=" O ALA G 851 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 24 Processing helix chain 'H' and resid 27 through 45 removed outlier: 4.348A pdb=" N LYS H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 58 removed outlier: 3.897A pdb=" N LEU H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 80 Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'H' and resid 143 through 159 Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.525A pdb=" N VAL H 199 " --> pdb=" O GLY H 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 240 removed outlier: 3.720A pdb=" N ALA H 230 " --> pdb=" O ASP H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 244 Processing helix chain 'H' and resid 258 through 268 removed outlier: 3.651A pdb=" N VAL H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 287 removed outlier: 3.886A pdb=" N ASP H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 removed outlier: 4.067A pdb=" N ILE H 296 " --> pdb=" O ASN H 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL H 297 " --> pdb=" O ALA H 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 293 through 297' Processing helix chain 'H' and resid 300 through 309 Processing helix chain 'H' and resid 349 through 365 removed outlier: 4.034A pdb=" N ILE H 363 " --> pdb=" O THR H 359 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY H 364 " --> pdb=" O MET H 360 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 365 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 390 removed outlier: 3.631A pdb=" N ILE H 383 " --> pdb=" O ASN H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 438 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.655A pdb=" N THR A 99 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 91 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 97 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 395 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 444 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL B 397 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA A 446 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER B 370 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR B 373 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 220 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 217 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA B 252 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 219 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL B 254 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 221 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN B 250 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE B 345 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 252 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 319 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 344 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG B 346 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS B 272 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE A 107 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 137 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 109 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 106 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE A 190 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS A 108 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A 192 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 110 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE A 210 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS A 272 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 319 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 344 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A 346 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 250 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE A 345 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 252 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 217 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A 252 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 219 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 254 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 221 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR A 373 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 220 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 370 " --> pdb=" O LEU A 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER A 460 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 633 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 462 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 595 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 482 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU A 542 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 484 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 607 through 611 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 92 removed outlier: 6.654A pdb=" N THR B 99 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 91 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 97 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.564A pdb=" N ILE B 107 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 137 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 109 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 106 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE B 190 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS B 108 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA B 192 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 110 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE B 210 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER B 460 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 633 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B 462 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 595 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 482 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 542 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 484 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 607 through 611 Processing sheet with id=AB1, first strand: chain 'C' and resid 88 through 92 removed outlier: 6.655A pdb=" N THR C 99 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU C 91 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 97 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 397 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER D 370 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR D 373 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 220 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 217 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA D 252 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 219 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL D 254 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 221 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 250 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE D 345 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA D 252 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 319 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU D 344 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY D 321 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ARG D 346 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS D 272 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE C 107 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 137 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY C 109 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 106 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE C 190 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS C 108 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA C 192 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 110 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE C 210 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 190 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL C 212 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA C 192 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS C 272 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU C 319 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU C 344 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY C 321 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG C 346 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN C 250 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE C 345 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 252 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 217 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 252 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 219 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL C 254 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 221 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR C 373 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 220 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 370 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 397 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 97 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU D 91 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 99 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 460 through 463 removed outlier: 6.406A pdb=" N SER C 460 " --> pdb=" O ALA C 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 633 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C 462 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 595 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 482 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU C 542 " --> pdb=" O PHE C 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 484 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 607 through 611 Processing sheet with id=AB6, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.562A pdb=" N ILE D 107 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER D 137 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY D 109 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 106 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE D 190 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS D 108 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA D 192 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 110 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE D 210 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE D 190 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL D 212 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA D 192 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 481 through 484 removed outlier: 6.451A pdb=" N PHE D 482 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 542 " --> pdb=" O PHE D 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 484 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D 595 " --> pdb=" O ILE D 632 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER D 460 " --> pdb=" O ALA D 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL D 633 " --> pdb=" O SER D 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR D 462 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE D 461 " --> pdb=" O HIS E 455 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS E 455 " --> pdb=" O ILE D 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 607 through 611 Processing sheet with id=AB9, first strand: chain 'E' and resid 88 through 92 removed outlier: 6.654A pdb=" N THR E 99 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU E 91 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 97 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 395 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 446 " --> pdb=" O ILE F 395 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL F 397 " --> pdb=" O ALA E 446 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER F 370 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR F 373 " --> pdb=" O PRO F 218 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 220 " --> pdb=" O TYR F 373 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL F 217 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA F 252 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 219 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL F 254 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE F 221 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN F 250 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE F 345 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 252 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU F 319 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU F 344 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY F 321 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG F 346 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS F 272 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE E 107 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER E 137 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY E 109 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE E 106 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE E 190 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS E 108 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA E 192 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 110 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ILE E 210 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 190 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL E 212 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA E 192 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS E 272 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 319 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU E 344 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY E 321 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG E 346 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN E 250 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE E 345 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA E 252 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 217 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA E 252 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL E 219 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL E 254 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 221 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR E 373 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 220 " --> pdb=" O TYR E 373 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER E 370 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE E 395 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR F 97 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU F 91 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR F 99 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER E 460 " --> pdb=" O ALA E 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL E 633 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR E 462 " --> pdb=" O VAL E 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 595 " --> pdb=" O ILE E 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E 482 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 542 " --> pdb=" O PHE E 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 484 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 607 through 611 Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.562A pdb=" N ILE F 107 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER F 137 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY F 109 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 106 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 190 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS F 108 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA F 192 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE F 110 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE F 210 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 190 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL F 212 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA F 192 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER F 460 " --> pdb=" O ALA F 631 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL F 633 " --> pdb=" O SER F 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR F 462 " --> pdb=" O VAL F 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F 595 " --> pdb=" O ILE F 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE F 482 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU F 542 " --> pdb=" O PHE F 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 484 " --> pdb=" O LEU F 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 607 through 611 Processing sheet with id=AC8, first strand: chain 'G' and resid 460 through 462 removed outlier: 3.597A pdb=" N THR G 595 " --> pdb=" O ILE G 632 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE G 539 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE G 594 " --> pdb=" O ILE G 539 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA G 541 " --> pdb=" O ILE G 594 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE G 482 " --> pdb=" O LEU G 540 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU G 542 " --> pdb=" O PHE G 482 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 484 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 483 " --> pdb=" O PHE G 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 607 through 611 Processing sheet with id=AD1, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.125A pdb=" N ILE H 88 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA H 101 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 167 through 169 removed outlier: 6.290A pdb=" N ILE H 134 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR H 193 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE H 190 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL H 212 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA H 192 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 272 through 274 removed outlier: 6.693A pdb=" N HIS H 272 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN H 250 " --> pdb=" O GLY H 343 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE H 345 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA H 252 " --> pdb=" O PHE H 345 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 217 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE H 253 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL H 219 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR H 373 " --> pdb=" O PRO H 218 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL H 220 " --> pdb=" O TYR H 373 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER H 370 " --> pdb=" O LEU H 396 " (cutoff:3.500A) 2081 hydrogen bonds defined for protein. 6132 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: 10.71 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15081 1.34 - 1.46: 9924 1.46 - 1.59: 21482 1.59 - 1.71: 6 1.71 - 1.83: 357 Bond restraints: 46850 Sorted by residual: bond pdb=" CG GLU G 590 " pdb=" CD GLU G 590 " ideal model delta sigma weight residual 1.516 1.411 0.105 2.50e-02 1.60e+03 1.78e+01 bond pdb=" CG GLU B 90 " pdb=" CD GLU B 90 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.35e+01 bond pdb=" CG GLU E 90 " pdb=" CD GLU E 90 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU F 90 " pdb=" CD GLU F 90 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU C 90 " pdb=" CD GLU C 90 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.32e+01 ... (remaining 46845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.46: 63023 6.46 - 12.91: 450 12.91 - 19.37: 45 19.37 - 25.82: 12 25.82 - 32.28: 6 Bond angle restraints: 63536 Sorted by residual: angle pdb=" CB ARG C 464 " pdb=" CG ARG C 464 " pdb=" CD ARG C 464 " ideal model delta sigma weight residual 111.30 143.58 -32.28 2.30e+00 1.89e-01 1.97e+02 angle pdb=" CB ARG D 464 " pdb=" CG ARG D 464 " pdb=" CD ARG D 464 " ideal model delta sigma weight residual 111.30 143.54 -32.24 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG E 464 " pdb=" CG ARG E 464 " pdb=" CD ARG E 464 " ideal model delta sigma weight residual 111.30 143.52 -32.22 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG F 464 " pdb=" CG ARG F 464 " pdb=" CD ARG F 464 " ideal model delta sigma weight residual 111.30 143.51 -32.21 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG A 464 " pdb=" CG ARG A 464 " pdb=" CD ARG A 464 " ideal model delta sigma weight residual 111.30 143.50 -32.20 2.30e+00 1.89e-01 1.96e+02 ... (remaining 63531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 24260 17.17 - 34.35: 2703 34.35 - 51.52: 1042 51.52 - 68.70: 320 68.70 - 85.87: 31 Dihedral angle restraints: 28356 sinusoidal: 10864 harmonic: 17492 Sorted by residual: dihedral pdb=" CA LYS C 447 " pdb=" C LYS C 447 " pdb=" N ARG C 448 " pdb=" CA ARG C 448 " ideal model delta harmonic sigma weight residual 180.00 135.12 44.88 0 5.00e+00 4.00e-02 8.06e+01 dihedral pdb=" CA LYS E 447 " pdb=" C LYS E 447 " pdb=" N ARG E 448 " pdb=" CA ARG E 448 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA LYS B 447 " pdb=" C LYS B 447 " pdb=" N ARG B 448 " pdb=" CA ARG B 448 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 28353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 6850 0.118 - 0.236: 410 0.236 - 0.353: 31 0.353 - 0.471: 18 0.471 - 0.589: 6 Chirality restraints: 7315 Sorted by residual: chirality pdb=" CB ILE A 67 " pdb=" CA ILE A 67 " pdb=" CG1 ILE A 67 " pdb=" CG2 ILE A 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CB ILE F 67 " pdb=" CA ILE F 67 " pdb=" CG1 ILE F 67 " pdb=" CG2 ILE F 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.65e+00 ... (remaining 7312 not shown) Planarity restraints: 8252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 90 " -0.041 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" CD GLU F 90 " 0.138 2.00e-02 2.50e+03 pdb=" OE1 GLU F 90 " -0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU F 90 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 90 " 0.041 2.00e-02 2.50e+03 7.94e-02 6.30e+01 pdb=" CD GLU D 90 " -0.137 2.00e-02 2.50e+03 pdb=" OE1 GLU D 90 " 0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU D 90 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 90 " -0.041 2.00e-02 2.50e+03 7.93e-02 6.29e+01 pdb=" CD GLU B 90 " 0.137 2.00e-02 2.50e+03 pdb=" OE1 GLU B 90 " -0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU B 90 " -0.048 2.00e-02 2.50e+03 ... (remaining 8249 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1111 2.57 - 3.16: 45926 3.16 - 3.74: 78832 3.74 - 4.32: 107218 4.32 - 4.90: 159755 Nonbonded interactions: 392842 Sorted by model distance: nonbonded pdb=" N GLN C 44 " pdb=" OE1 GLN C 44 " model vdw 1.992 3.120 nonbonded pdb=" N GLN B 44 " pdb=" OE1 GLN B 44 " model vdw 1.992 3.120 nonbonded pdb=" N GLN D 44 " pdb=" OE1 GLN D 44 " model vdw 1.993 3.120 nonbonded pdb=" N GLN A 44 " pdb=" OE1 GLN A 44 " model vdw 1.993 3.120 nonbonded pdb=" N GLN E 44 " pdb=" OE1 GLN E 44 " model vdw 1.993 3.120 ... (remaining 392837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 41.930 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.007 0.111 46850 Z= 0.357 Angle : 1.472 32.280 63536 Z= 0.772 Chirality : 0.067 0.589 7315 Planarity : 0.007 0.087 8252 Dihedral : 17.807 85.869 17100 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 39.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 15.66 % Allowed : 8.84 % Favored : 75.50 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 2.26 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.10), residues: 6053 helix: -1.53 (0.09), residues: 2702 sheet: -1.66 (0.16), residues: 964 loop : -2.52 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.004 ARG G 464 TYR 0.049 0.004 TYR C 259 PHE 0.048 0.004 PHE C 824 TRP 0.088 0.008 TRP B 425 HIS 0.012 0.002 HIS F 780 Details of bonding type rmsd covalent geometry : bond 0.00746 (46850) covalent geometry : angle 1.47235 (63536) hydrogen bonds : bond 0.17021 ( 2081) hydrogen bonds : angle 8.27144 ( 6132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 753 poor density : 653 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7840 (ppp) REVERT: A 386 PHE cc_start: 0.8926 (t80) cc_final: 0.8627 (t80) REVERT: A 413 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: A 452 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3258 (tpp) REVERT: A 464 ARG cc_start: -0.2464 (OUTLIER) cc_final: -0.2967 (mtm110) REVERT: A 548 MET cc_start: -0.0075 (OUTLIER) cc_final: -0.0436 (mtt) REVERT: A 557 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.4971 (mmm) REVERT: A 582 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8414 (m-10) REVERT: A 585 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8622 (mpp) REVERT: A 614 LYS cc_start: 0.9389 (mptt) cc_final: 0.8908 (pttp) REVERT: A 708 ILE cc_start: 0.2480 (OUTLIER) cc_final: 0.2189 (mm) REVERT: B 86 CYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5841 (m) REVERT: B 523 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 531 MET cc_start: 0.9262 (ppp) cc_final: 0.8792 (ppp) REVERT: B 718 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4453 (pp) REVERT: C 46 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (ptp-170) REVERT: C 76 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 123 LYS cc_start: 0.8988 (mttt) cc_final: 0.8637 (mtpt) REVERT: C 182 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8597 (ptm) REVERT: C 233 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8970 (p) REVERT: C 238 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7748 (tptt) REVERT: C 413 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: C 452 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7006 (tpp) REVERT: D 22 GLU cc_start: 0.8827 (pm20) cc_final: 0.8542 (pm20) REVERT: D 452 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.4711 (tpp) REVERT: D 618 LYS cc_start: 0.5434 (tttt) cc_final: 0.4811 (mttt) REVERT: D 638 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8595 (p) REVERT: E 89 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8897 (mm) REVERT: E 198 MET cc_start: 0.9664 (mmp) cc_final: 0.9331 (mtt) REVERT: E 296 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (mp) REVERT: E 360 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9222 (mmm) REVERT: E 389 LYS cc_start: 0.3302 (OUTLIER) cc_final: 0.2762 (ttpt) REVERT: E 390 LEU cc_start: 0.6132 (mm) cc_final: 0.5556 (mm) REVERT: E 478 LYS cc_start: 0.6856 (mppt) cc_final: 0.6505 (mtmm) REVERT: E 523 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8184 (p) REVERT: E 554 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: E 613 ASP cc_start: 0.7870 (m-30) cc_final: 0.7365 (m-30) REVERT: E 680 MET cc_start: 0.8285 (ppp) cc_final: 0.7868 (ppp) REVERT: E 751 ASN cc_start: 0.8553 (m-40) cc_final: 0.8210 (t0) REVERT: F 46 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8247 (ptt180) REVERT: F 89 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9071 (mt) REVERT: F 182 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: F 198 MET cc_start: 0.9163 (mmp) cc_final: 0.8873 (mtp) REVERT: F 260 ASP cc_start: 0.9495 (OUTLIER) cc_final: 0.9232 (p0) REVERT: F 272 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (m-70) REVERT: F 307 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8422 (ptt) REVERT: F 413 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9107 (p0) REVERT: F 442 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (mmmt) REVERT: F 452 MET cc_start: 0.3730 (OUTLIER) cc_final: 0.3371 (tpt) REVERT: F 552 LYS cc_start: 0.9455 (mttt) cc_final: 0.9214 (mttt) REVERT: F 573 MET cc_start: 0.5702 (mtm) cc_final: 0.3324 (tmm) REVERT: F 585 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6348 (pmm) REVERT: G 566 GLU cc_start: 0.9188 (mp0) cc_final: 0.8960 (mp0) REVERT: G 570 MET cc_start: 0.8774 (tpt) cc_final: 0.8412 (ttt) REVERT: G 573 MET cc_start: 0.1689 (tmm) cc_final: 0.1014 (tpt) REVERT: G 580 TYR cc_start: 0.8490 (m-80) cc_final: 0.8186 (m-80) REVERT: G 581 LYS cc_start: 0.9719 (mtmm) cc_final: 0.9375 (tmtt) REVERT: G 691 ASN cc_start: 0.8709 (m-40) cc_final: 0.8258 (m-40) REVERT: H 78 ASN cc_start: 0.9250 (m-40) cc_final: 0.8855 (t0) outliers start: 753 outliers final: 170 residues processed: 1155 average time/residue: 0.2871 time to fit residues: 538.5024 Evaluate side-chains 648 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 441 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 597 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 172 GLN A 272 HIS A 560 HIS A 636 ASN ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS A 736 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 HIS A 792 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 272 HIS B 356 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 HIS B 736 HIS ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN B 807 ASN C 30 GLN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 272 HIS C 560 HIS ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN D 30 GLN D 132 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 HIS D 736 HIS ** D 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 HIS D 792 GLN E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 HIS ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 GLN E 560 HIS ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 715 ASN ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 HIS E 792 GLN E 807 ASN F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 676 GLN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 HIS F 736 HIS ** F 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 780 HIS ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 722 HIS G 736 HIS ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 792 GLN H 70 HIS ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.084134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.067842 restraints weight = 477938.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.069135 restraints weight = 308828.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070044 restraints weight = 221981.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.070766 restraints weight = 173215.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.071256 restraints weight = 142339.989| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 46850 Z= 0.200 Angle : 0.853 13.009 63536 Z= 0.439 Chirality : 0.049 0.289 7315 Planarity : 0.006 0.135 8252 Dihedral : 6.641 39.959 6439 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.40 % Allowed : 5.16 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 2.26 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.10), residues: 6053 helix: -0.81 (0.09), residues: 2780 sheet: -1.36 (0.16), residues: 977 loop : -2.42 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 487 TYR 0.027 0.003 TYR F 684 PHE 0.033 0.002 PHE C 35 TRP 0.038 0.003 TRP A 425 HIS 0.008 0.002 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00434 (46850) covalent geometry : angle 0.85253 (63536) hydrogen bonds : bond 0.05510 ( 2081) hydrogen bonds : angle 5.87139 ( 6132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 575 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.9306 (ptp) cc_final: 0.8336 (tmm) REVERT: A 307 MET cc_start: 0.8172 (ppp) cc_final: 0.7900 (ppp) REVERT: A 383 ILE cc_start: 0.8810 (mt) cc_final: 0.8597 (mm) REVERT: A 386 PHE cc_start: 0.8964 (t80) cc_final: 0.8548 (t80) REVERT: A 639 MET cc_start: 0.1662 (mmt) cc_final: 0.0873 (mmt) REVERT: B 445 VAL cc_start: 0.8626 (t) cc_final: 0.8360 (t) REVERT: B 457 LEU cc_start: 0.9447 (mm) cc_final: 0.9203 (pt) REVERT: B 531 MET cc_start: 0.9275 (ppp) cc_final: 0.9038 (ppp) REVERT: B 535 GLN cc_start: 0.9742 (mm-40) cc_final: 0.9529 (mm-40) REVERT: B 580 TYR cc_start: 0.8576 (m-80) cc_final: 0.8343 (m-80) REVERT: B 630 MET cc_start: 0.8701 (tpt) cc_final: 0.8291 (tpp) REVERT: C 59 MET cc_start: 0.5886 (ptp) cc_final: 0.5382 (ptp) REVERT: C 77 TYR cc_start: 0.9151 (t80) cc_final: 0.8910 (t80) REVERT: C 98 MET cc_start: 0.9133 (mmp) cc_final: 0.8926 (mmp) REVERT: C 123 LYS cc_start: 0.9600 (mttt) cc_final: 0.9242 (mtpt) REVERT: C 182 MET cc_start: 0.9235 (ttt) cc_final: 0.8652 (ptm) REVERT: C 554 MET cc_start: 0.9698 (ptp) cc_final: 0.9348 (mtt) REVERT: C 557 MET cc_start: 0.9624 (mmp) cc_final: 0.9415 (mmm) REVERT: C 570 MET cc_start: 0.9265 (mtt) cc_final: 0.8934 (mtp) REVERT: C 582 PHE cc_start: 0.9325 (m-80) cc_final: 0.9097 (m-80) REVERT: C 618 LYS cc_start: 0.9100 (tttt) cc_final: 0.8898 (tttt) REVERT: C 630 MET cc_start: 0.9726 (tpt) cc_final: 0.9433 (tpp) REVERT: C 829 ASP cc_start: 0.9533 (OUTLIER) cc_final: 0.9047 (p0) REVERT: D 91 GLU cc_start: 0.8124 (mp0) cc_final: 0.7734 (mp0) REVERT: D 122 PHE cc_start: 0.9664 (t80) cc_final: 0.9430 (t80) REVERT: D 135 ILE cc_start: 0.9536 (mm) cc_final: 0.9241 (tp) REVERT: D 182 MET cc_start: 0.9323 (ppp) cc_final: 0.9038 (ppp) REVERT: D 262 VAL cc_start: 0.9816 (t) cc_final: 0.9542 (p) REVERT: D 452 MET cc_start: 0.6057 (tpp) cc_final: 0.5467 (tpp) REVERT: D 483 LEU cc_start: 0.8936 (tp) cc_final: 0.8645 (tp) REVERT: D 518 ASP cc_start: 0.8647 (t0) cc_final: 0.8275 (t0) REVERT: D 580 TYR cc_start: 0.8549 (m-80) cc_final: 0.8347 (m-80) REVERT: D 639 MET cc_start: 0.9281 (pmm) cc_final: 0.9055 (pmm) REVERT: E 182 MET cc_start: 0.6775 (ppp) cc_final: 0.6293 (ppp) REVERT: E 266 PHE cc_start: 0.9451 (m-10) cc_final: 0.9201 (m-10) REVERT: E 307 MET cc_start: 0.8281 (ppp) cc_final: 0.7905 (ppp) REVERT: E 360 MET cc_start: 0.9643 (mmm) cc_final: 0.9331 (ttp) REVERT: E 383 ILE cc_start: 0.8562 (mt) cc_final: 0.8357 (mm) REVERT: E 390 LEU cc_start: 0.6640 (mm) cc_final: 0.6358 (mm) REVERT: E 462 TYR cc_start: 0.8945 (m-80) cc_final: 0.8603 (m-10) REVERT: E 557 MET cc_start: 0.9823 (mtm) cc_final: 0.9321 (tpp) REVERT: E 573 MET cc_start: 0.8750 (mmm) cc_final: 0.8502 (mmm) REVERT: E 613 ASP cc_start: 0.7289 (m-30) cc_final: 0.6972 (m-30) REVERT: E 619 TYR cc_start: 0.9399 (m-80) cc_final: 0.9063 (m-80) REVERT: E 680 MET cc_start: 0.9225 (ppp) cc_final: 0.9005 (ppp) REVERT: E 751 ASN cc_start: 0.8983 (m-40) cc_final: 0.8779 (t0) REVERT: E 797 LEU cc_start: 0.9678 (tt) cc_final: 0.9228 (mt) REVERT: F 182 MET cc_start: 0.8962 (ttt) cc_final: 0.8632 (ppp) REVERT: F 307 MET cc_start: 0.8690 (ppp) cc_final: 0.8405 (ppp) REVERT: F 573 MET cc_start: 0.5343 (mtm) cc_final: 0.3341 (tmm) REVERT: F 580 TYR cc_start: 0.9226 (m-80) cc_final: 0.9008 (m-80) REVERT: G 512 PHE cc_start: 0.7440 (t80) cc_final: 0.6976 (t80) REVERT: G 524 VAL cc_start: 0.9030 (m) cc_final: 0.8295 (p) REVERT: G 572 PHE cc_start: 0.8163 (m-80) cc_final: 0.7730 (m-80) REVERT: G 581 LYS cc_start: 0.9580 (mtmm) cc_final: 0.9370 (tmtt) REVERT: G 636 ASN cc_start: 0.7350 (p0) cc_final: 0.6982 (p0) REVERT: H 80 TYR cc_start: 0.9062 (m-10) cc_final: 0.8756 (m-80) outliers start: 19 outliers final: 0 residues processed: 594 average time/residue: 0.2855 time to fit residues: 278.1802 Evaluate side-chains 412 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 381 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 435 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 164 optimal weight: 20.0000 chunk 314 optimal weight: 0.0270 chunk 29 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 overall best weight: 2.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 715 ASN A 807 ASN B 20 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 HIS B 636 ASN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN C 722 HIS C 736 HIS C 807 ASN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN E 398 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 722 HIS E 736 HIS ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 ASN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 759 GLN G 792 GLN ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.083753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067722 restraints weight = 479160.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.069084 restraints weight = 308632.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.069854 restraints weight = 216740.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.070733 restraints weight = 167533.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.071120 restraints weight = 136297.618| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 46850 Z= 0.149 Angle : 0.735 13.116 63536 Z= 0.374 Chirality : 0.047 0.296 7315 Planarity : 0.005 0.086 8252 Dihedral : 5.815 35.569 6439 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.27 % Allowed : 4.41 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 1.13 % 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: -1.79 (0.11), residues: 6053 helix: -0.25 (0.10), residues: 2764 sheet: -1.33 (0.16), residues: 975 loop : -2.20 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG H 36 TYR 0.023 0.002 TYR E 77 PHE 0.021 0.002 PHE D 565 TRP 0.025 0.002 TRP G 555 HIS 0.008 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00324 (46850) covalent geometry : angle 0.73543 (63536) hydrogen bonds : bond 0.04555 ( 2081) hydrogen bonds : angle 5.24844 ( 6132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 531 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.9333 (ptp) cc_final: 0.9128 (ppp) REVERT: A 307 MET cc_start: 0.8097 (ppp) cc_final: 0.7798 (ppp) REVERT: A 507 MET cc_start: 0.6880 (mtp) cc_final: 0.6578 (ttt) REVERT: A 639 MET cc_start: 0.1562 (mmt) cc_final: 0.0759 (mmt) REVERT: A 641 MET cc_start: 0.6759 (ptt) cc_final: 0.6268 (ptt) REVERT: A 785 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8542 (tt0) REVERT: B 198 MET cc_start: 0.7775 (ptt) cc_final: 0.6876 (tpt) REVERT: B 386 PHE cc_start: 0.9429 (t80) cc_final: 0.9013 (t80) REVERT: B 445 VAL cc_start: 0.8809 (t) cc_final: 0.8554 (t) REVERT: B 531 MET cc_start: 0.9288 (ppp) cc_final: 0.8977 (ppp) REVERT: B 535 GLN cc_start: 0.9744 (mm-40) cc_final: 0.9534 (mm-40) REVERT: B 557 MET cc_start: 0.9628 (mmp) cc_final: 0.9396 (mmm) REVERT: B 630 MET cc_start: 0.8691 (tpt) cc_final: 0.8255 (tpp) REVERT: C 59 MET cc_start: 0.6487 (ptp) cc_final: 0.6042 (ptp) REVERT: C 68 LYS cc_start: 0.9511 (pttp) cc_final: 0.9220 (pptt) REVERT: C 79 LYS cc_start: 0.9438 (tptt) cc_final: 0.9219 (mmmm) REVERT: C 98 MET cc_start: 0.9076 (mmp) cc_final: 0.8825 (mmp) REVERT: C 123 LYS cc_start: 0.9567 (mttt) cc_final: 0.8993 (ptmt) REVERT: C 182 MET cc_start: 0.9193 (ttt) cc_final: 0.8628 (ptm) REVERT: C 307 MET cc_start: 0.9636 (ptt) cc_final: 0.9140 (ppp) REVERT: C 442 LYS cc_start: 0.9411 (mmpt) cc_final: 0.9189 (tppt) REVERT: C 554 MET cc_start: 0.9652 (ptp) cc_final: 0.9424 (mtt) REVERT: C 557 MET cc_start: 0.9625 (mmp) cc_final: 0.9343 (mmm) REVERT: C 585 MET cc_start: 0.7293 (mmt) cc_final: 0.6913 (mmt) REVERT: C 630 MET cc_start: 0.9727 (tpt) cc_final: 0.9454 (tpp) REVERT: D 135 ILE cc_start: 0.9542 (mm) cc_final: 0.9260 (tp) REVERT: D 182 MET cc_start: 0.9367 (ppp) cc_final: 0.9100 (ppp) REVERT: D 262 VAL cc_start: 0.9760 (t) cc_final: 0.9524 (t) REVERT: D 452 MET cc_start: 0.6003 (tpp) cc_final: 0.5517 (tpt) REVERT: D 483 LEU cc_start: 0.9047 (tp) cc_final: 0.8803 (tp) REVERT: D 573 MET cc_start: 0.7890 (mmm) cc_final: 0.6854 (mmm) REVERT: D 574 ASP cc_start: 0.8880 (p0) cc_final: 0.8175 (m-30) REVERT: D 580 TYR cc_start: 0.8648 (m-80) cc_final: 0.8395 (m-80) REVERT: D 582 PHE cc_start: 0.8328 (m-80) cc_final: 0.7965 (m-80) REVERT: D 618 LYS cc_start: 0.6554 (tttt) cc_final: 0.5840 (mttt) REVERT: D 630 MET cc_start: 0.9380 (mmp) cc_final: 0.9108 (mmt) REVERT: D 717 PHE cc_start: 0.5242 (t80) cc_final: 0.4454 (t80) REVERT: D 774 TYR cc_start: 0.8648 (m-80) cc_final: 0.7981 (m-80) REVERT: D 824 PHE cc_start: 0.9167 (t80) cc_final: 0.8921 (t80) REVERT: E 182 MET cc_start: 0.6853 (ppp) cc_final: 0.6265 (ppp) REVERT: E 236 MET cc_start: 0.9397 (tmm) cc_final: 0.9190 (mmt) REVERT: E 266 PHE cc_start: 0.9539 (m-10) cc_final: 0.9280 (m-10) REVERT: E 307 MET cc_start: 0.8195 (ppp) cc_final: 0.7936 (ppp) REVERT: E 322 GLU cc_start: 0.7924 (tp30) cc_final: 0.7343 (mm-30) REVERT: E 360 MET cc_start: 0.9668 (mmm) cc_final: 0.9323 (ttp) REVERT: E 390 LEU cc_start: 0.6967 (mm) cc_final: 0.6623 (mm) REVERT: E 462 TYR cc_start: 0.9010 (m-80) cc_final: 0.8742 (m-10) REVERT: E 557 MET cc_start: 0.9809 (mtm) cc_final: 0.9414 (tpp) REVERT: E 564 HIS cc_start: 0.9103 (t-90) cc_final: 0.8765 (t-170) REVERT: E 613 ASP cc_start: 0.7264 (m-30) cc_final: 0.6965 (m-30) REVERT: E 619 TYR cc_start: 0.9421 (m-80) cc_final: 0.9085 (m-80) REVERT: E 680 MET cc_start: 0.9373 (ppp) cc_final: 0.9114 (ppp) REVERT: E 751 ASN cc_start: 0.8982 (m-40) cc_final: 0.8721 (t0) REVERT: E 797 LEU cc_start: 0.9674 (tt) cc_final: 0.9249 (mt) REVERT: F 182 MET cc_start: 0.9011 (ttt) cc_final: 0.8499 (ppp) REVERT: F 236 MET cc_start: 0.9458 (mmp) cc_final: 0.9129 (mmm) REVERT: F 307 MET cc_start: 0.8744 (ppp) cc_final: 0.8254 (ppp) REVERT: F 539 ILE cc_start: 0.9756 (pt) cc_final: 0.9490 (mm) REVERT: F 554 MET cc_start: 0.9732 (ppp) cc_final: 0.9422 (tmm) REVERT: F 563 THR cc_start: 0.7275 (t) cc_final: 0.7072 (t) REVERT: F 573 MET cc_start: 0.5114 (mtm) cc_final: 0.3307 (tmm) REVERT: F 580 TYR cc_start: 0.9139 (m-80) cc_final: 0.8936 (m-80) REVERT: G 512 PHE cc_start: 0.7547 (t80) cc_final: 0.7124 (t80) REVERT: G 524 VAL cc_start: 0.8874 (m) cc_final: 0.8202 (p) REVERT: G 570 MET cc_start: 0.6945 (ttt) cc_final: 0.6738 (ttt) REVERT: G 637 LEU cc_start: 0.8455 (mt) cc_final: 0.8190 (pp) REVERT: H 80 TYR cc_start: 0.9165 (m-10) cc_final: 0.8822 (m-80) outliers start: 13 outliers final: 3 residues processed: 543 average time/residue: 0.2629 time to fit residues: 234.9222 Evaluate side-chains 404 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 138 optimal weight: 0.0970 chunk 353 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 460 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 144 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 374 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN B 30 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 172 GLN C 535 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 216 ASN ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN E 398 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 GLN F 807 ASN G 691 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 792 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.081732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.065541 restraints weight = 487009.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.066747 restraints weight = 311404.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.067616 restraints weight = 218962.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.068285 restraints weight = 168053.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.068853 restraints weight = 138811.197| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46850 Z= 0.158 Angle : 0.711 13.363 63536 Z= 0.363 Chirality : 0.046 0.292 7315 Planarity : 0.005 0.075 8252 Dihedral : 5.470 33.698 6439 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 1.13 % 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: -1.57 (0.11), residues: 6053 helix: -0.10 (0.10), residues: 2835 sheet: -1.16 (0.17), residues: 935 loop : -2.12 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 464 TYR 0.020 0.002 TYR F 684 PHE 0.027 0.002 PHE C 345 TRP 0.027 0.002 TRP F 555 HIS 0.006 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00337 (46850) covalent geometry : angle 0.71051 (63536) hydrogen bonds : bond 0.04191 ( 2081) hydrogen bonds : angle 5.03607 ( 6132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 502 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.7869 (ptm) cc_final: 0.7438 (tmm) REVERT: A 182 MET cc_start: 0.9306 (ptp) cc_final: 0.9094 (ppp) REVERT: A 307 MET cc_start: 0.8047 (ppp) cc_final: 0.7796 (ppp) REVERT: A 383 ILE cc_start: 0.9046 (mt) cc_final: 0.8845 (mm) REVERT: A 507 MET cc_start: 0.6974 (mtp) cc_final: 0.6639 (ttt) REVERT: A 531 MET cc_start: 0.8146 (ttt) cc_final: 0.7749 (ttt) REVERT: A 639 MET cc_start: 0.0962 (mmt) cc_final: 0.0416 (mmt) REVERT: A 641 MET cc_start: 0.6735 (ptt) cc_final: 0.6237 (ptt) REVERT: A 785 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8479 (tt0) REVERT: B 198 MET cc_start: 0.7595 (ptt) cc_final: 0.6590 (tpt) REVERT: B 307 MET cc_start: -0.1133 (ptt) cc_final: -0.3356 (tpt) REVERT: B 386 PHE cc_start: 0.9355 (t80) cc_final: 0.8919 (t80) REVERT: B 445 VAL cc_start: 0.8892 (t) cc_final: 0.8666 (t) REVERT: B 531 MET cc_start: 0.9288 (ppp) cc_final: 0.9030 (ppp) REVERT: B 535 GLN cc_start: 0.9721 (mm-40) cc_final: 0.9403 (mp10) REVERT: B 557 MET cc_start: 0.9603 (mmp) cc_final: 0.9384 (mmm) REVERT: B 630 MET cc_start: 0.8701 (tpt) cc_final: 0.8202 (tpp) REVERT: C 68 LYS cc_start: 0.9485 (pttp) cc_final: 0.9141 (pptt) REVERT: C 79 LYS cc_start: 0.9553 (tptt) cc_final: 0.9320 (mmmm) REVERT: C 98 MET cc_start: 0.8777 (mmp) cc_final: 0.8433 (mmp) REVERT: C 123 LYS cc_start: 0.9597 (mttt) cc_final: 0.9172 (mtpt) REVERT: C 182 MET cc_start: 0.9182 (ttt) cc_final: 0.8689 (ptm) REVERT: C 307 MET cc_start: 0.9601 (ptt) cc_final: 0.9149 (ppp) REVERT: C 394 ARG cc_start: 0.9298 (mtm180) cc_final: 0.8643 (ptt180) REVERT: C 442 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9168 (tppt) REVERT: C 557 MET cc_start: 0.9667 (mmp) cc_final: 0.9328 (mmm) REVERT: C 570 MET cc_start: 0.9224 (mtt) cc_final: 0.8932 (mtt) REVERT: C 630 MET cc_start: 0.9732 (tpt) cc_final: 0.9383 (tpt) REVERT: C 823 ASP cc_start: 0.9452 (m-30) cc_final: 0.9166 (p0) REVERT: D 91 GLU cc_start: 0.8436 (mp0) cc_final: 0.8214 (mp0) REVERT: D 135 ILE cc_start: 0.9534 (mm) cc_final: 0.9231 (tp) REVERT: D 182 MET cc_start: 0.9389 (ppp) cc_final: 0.9133 (ppp) REVERT: D 262 VAL cc_start: 0.9805 (t) cc_final: 0.9405 (t) REVERT: D 266 PHE cc_start: 0.9314 (m-80) cc_final: 0.9088 (m-80) REVERT: D 452 MET cc_start: 0.6560 (tpp) cc_final: 0.6089 (tpt) REVERT: D 483 LEU cc_start: 0.9154 (tp) cc_final: 0.8932 (tp) REVERT: D 539 ILE cc_start: 0.9492 (mm) cc_final: 0.9270 (mp) REVERT: D 580 TYR cc_start: 0.8537 (m-80) cc_final: 0.8272 (m-80) REVERT: D 582 PHE cc_start: 0.8263 (m-80) cc_final: 0.7895 (m-80) REVERT: D 618 LYS cc_start: 0.6456 (tttt) cc_final: 0.5684 (mttt) REVERT: D 630 MET cc_start: 0.9438 (mmp) cc_final: 0.9195 (mmm) REVERT: D 639 MET cc_start: 0.9176 (pmm) cc_final: 0.8761 (pmm) REVERT: D 717 PHE cc_start: 0.5562 (t80) cc_final: 0.5002 (t80) REVERT: D 774 TYR cc_start: 0.8616 (m-80) cc_final: 0.7979 (m-80) REVERT: E 182 MET cc_start: 0.7178 (ppp) cc_final: 0.6455 (ppp) REVERT: E 266 PHE cc_start: 0.9482 (m-10) cc_final: 0.9206 (m-10) REVERT: E 307 MET cc_start: 0.8052 (ppp) cc_final: 0.7773 (ppp) REVERT: E 322 GLU cc_start: 0.7774 (tp30) cc_final: 0.7288 (mm-30) REVERT: E 360 MET cc_start: 0.9653 (mmm) cc_final: 0.9274 (mmm) REVERT: E 390 LEU cc_start: 0.7498 (mm) cc_final: 0.7139 (mm) REVERT: E 452 MET cc_start: 0.7717 (tpp) cc_final: 0.6854 (tpp) REVERT: E 548 MET cc_start: 0.9752 (ptp) cc_final: 0.9482 (mpp) REVERT: E 553 ILE cc_start: 0.9754 (mt) cc_final: 0.9473 (mt) REVERT: E 554 MET cc_start: 0.9293 (ppp) cc_final: 0.8674 (ppp) REVERT: E 557 MET cc_start: 0.9773 (mtm) cc_final: 0.9539 (mtt) REVERT: E 564 HIS cc_start: 0.9022 (t-90) cc_final: 0.8704 (t-170) REVERT: E 573 MET cc_start: 0.8817 (mmm) cc_final: 0.8502 (mmm) REVERT: E 613 ASP cc_start: 0.7680 (m-30) cc_final: 0.7468 (m-30) REVERT: E 680 MET cc_start: 0.9298 (ppp) cc_final: 0.8969 (ppp) REVERT: E 751 ASN cc_start: 0.8909 (m-40) cc_final: 0.8653 (t0) REVERT: F 182 MET cc_start: 0.9114 (ttt) cc_final: 0.8527 (ppp) REVERT: F 236 MET cc_start: 0.9406 (mmp) cc_final: 0.9105 (mmm) REVERT: F 307 MET cc_start: 0.8851 (ppp) cc_final: 0.8259 (ppp) REVERT: F 342 LEU cc_start: 0.9441 (tp) cc_final: 0.9181 (tp) REVERT: F 563 THR cc_start: 0.7492 (t) cc_final: 0.7278 (t) REVERT: F 573 MET cc_start: 0.5436 (mtm) cc_final: 0.3528 (tmm) REVERT: F 585 MET cc_start: 0.8441 (tpt) cc_final: 0.7349 (tpt) REVERT: F 590 GLU cc_start: 0.9646 (mp0) cc_final: 0.9415 (mp0) REVERT: F 591 LEU cc_start: 0.8951 (tp) cc_final: 0.8676 (tp) REVERT: F 630 MET cc_start: 0.9391 (tpt) cc_final: 0.9180 (tpp) REVERT: G 452 MET cc_start: 0.3854 (tmm) cc_final: 0.3558 (tmm) REVERT: G 512 PHE cc_start: 0.7570 (t80) cc_final: 0.7039 (t80) REVERT: G 524 VAL cc_start: 0.8808 (m) cc_final: 0.8185 (p) REVERT: G 572 PHE cc_start: 0.8422 (m-10) cc_final: 0.7805 (m-80) REVERT: G 637 LEU cc_start: 0.8487 (mt) cc_final: 0.8136 (pp) REVERT: H 80 TYR cc_start: 0.9105 (m-10) cc_final: 0.8762 (m-80) outliers start: 8 outliers final: 0 residues processed: 508 average time/residue: 0.2457 time to fit residues: 207.5241 Evaluate side-chains 375 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 261 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 278 optimal weight: 9.9990 chunk 470 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 391 optimal weight: 9.9990 chunk 344 optimal weight: 50.0000 chunk 513 optimal weight: 8.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 78 ASN ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 20 GLN C 30 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 94 ASN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS E 132 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN F 242 ASN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 807 ASN G 691 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 759 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.079395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.063132 restraints weight = 487088.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.064352 restraints weight = 310161.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.065180 restraints weight = 221561.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.065892 restraints weight = 172194.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.066438 restraints weight = 141005.877| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 46850 Z= 0.179 Angle : 0.717 12.887 63536 Z= 0.369 Chirality : 0.047 0.291 7315 Planarity : 0.005 0.071 8252 Dihedral : 5.308 32.012 6439 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.75 % 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: -1.49 (0.11), residues: 6053 helix: -0.03 (0.10), residues: 2854 sheet: -1.02 (0.17), residues: 899 loop : -2.13 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 46 TYR 0.025 0.002 TYR G 462 PHE 0.031 0.002 PHE A 75 TRP 0.028 0.002 TRP G 555 HIS 0.009 0.001 HIS E 70 Details of bonding type rmsd covalent geometry : bond 0.00374 (46850) covalent geometry : angle 0.71686 (63536) hydrogen bonds : bond 0.04074 ( 2081) hydrogen bonds : angle 4.95018 ( 6132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.9374 (ptp) cc_final: 0.8503 (tmm) REVERT: A 307 MET cc_start: 0.8171 (ppp) cc_final: 0.7924 (ppp) REVERT: A 383 ILE cc_start: 0.8993 (mt) cc_final: 0.8727 (mm) REVERT: A 396 LEU cc_start: 0.9085 (mm) cc_final: 0.8638 (tp) REVERT: A 507 MET cc_start: 0.7181 (mtp) cc_final: 0.6884 (ttt) REVERT: A 531 MET cc_start: 0.8652 (ttt) cc_final: 0.8340 (ttt) REVERT: A 639 MET cc_start: 0.0980 (mmt) cc_final: 0.0117 (mmt) REVERT: A 641 MET cc_start: 0.7308 (ptt) cc_final: 0.6886 (ptt) REVERT: B 198 MET cc_start: 0.7851 (ptt) cc_final: 0.6914 (tpt) REVERT: B 307 MET cc_start: -0.0722 (ptt) cc_final: -0.2984 (tpt) REVERT: B 386 PHE cc_start: 0.9306 (t80) cc_final: 0.9016 (t80) REVERT: B 445 VAL cc_start: 0.9069 (t) cc_final: 0.8830 (t) REVERT: B 531 MET cc_start: 0.9127 (ppp) cc_final: 0.8910 (ppp) REVERT: B 630 MET cc_start: 0.8801 (tpt) cc_final: 0.8307 (tpp) REVERT: C 59 MET cc_start: 0.7068 (ptp) cc_final: 0.6701 (ptp) REVERT: C 68 LYS cc_start: 0.9518 (pttp) cc_final: 0.9187 (pptt) REVERT: C 79 LYS cc_start: 0.9582 (tptt) cc_final: 0.9358 (mmmm) REVERT: C 98 MET cc_start: 0.8808 (mmp) cc_final: 0.8531 (mmp) REVERT: C 123 LYS cc_start: 0.9602 (mttt) cc_final: 0.9168 (mtpt) REVERT: C 182 MET cc_start: 0.9282 (ttt) cc_final: 0.8841 (ptm) REVERT: C 307 MET cc_start: 0.9706 (ptt) cc_final: 0.9313 (ppp) REVERT: C 394 ARG cc_start: 0.9366 (mtm180) cc_final: 0.8726 (ptt180) REVERT: C 542 LEU cc_start: 0.9600 (tp) cc_final: 0.9294 (mm) REVERT: C 557 MET cc_start: 0.9737 (mmp) cc_final: 0.9424 (mmm) REVERT: C 630 MET cc_start: 0.9736 (tpt) cc_final: 0.9369 (tpt) REVERT: C 823 ASP cc_start: 0.9528 (m-30) cc_final: 0.9223 (p0) REVERT: D 182 MET cc_start: 0.9378 (ppp) cc_final: 0.9141 (ppp) REVERT: D 262 VAL cc_start: 0.9826 (t) cc_final: 0.9438 (t) REVERT: D 266 PHE cc_start: 0.9462 (m-80) cc_final: 0.9203 (m-80) REVERT: D 452 MET cc_start: 0.6767 (tpp) cc_final: 0.6530 (tpt) REVERT: D 580 TYR cc_start: 0.8691 (m-80) cc_final: 0.8370 (m-80) REVERT: D 582 PHE cc_start: 0.8311 (m-80) cc_final: 0.7860 (m-80) REVERT: D 618 LYS cc_start: 0.6852 (tttt) cc_final: 0.6511 (tttt) REVERT: D 639 MET cc_start: 0.9271 (pmm) cc_final: 0.9026 (pmm) REVERT: D 717 PHE cc_start: 0.5958 (t80) cc_final: 0.5171 (t80) REVERT: D 824 PHE cc_start: 0.9163 (t80) cc_final: 0.8946 (t80) REVERT: E 136 PHE cc_start: 0.9108 (m-80) cc_final: 0.8866 (m-10) REVERT: E 182 MET cc_start: 0.7338 (ppp) cc_final: 0.6687 (ppp) REVERT: E 266 PHE cc_start: 0.9571 (m-10) cc_final: 0.9311 (m-10) REVERT: E 307 MET cc_start: 0.8207 (ppp) cc_final: 0.7831 (ppp) REVERT: E 322 GLU cc_start: 0.7855 (tp30) cc_final: 0.7366 (mm-30) REVERT: E 360 MET cc_start: 0.9725 (mmm) cc_final: 0.9347 (mmm) REVERT: E 390 LEU cc_start: 0.7648 (mm) cc_final: 0.7304 (mm) REVERT: E 452 MET cc_start: 0.6903 (tpp) cc_final: 0.6534 (tpp) REVERT: E 554 MET cc_start: 0.9338 (ppp) cc_final: 0.8466 (ptm) REVERT: E 557 MET cc_start: 0.9807 (mtm) cc_final: 0.9584 (mtt) REVERT: E 564 HIS cc_start: 0.9049 (t-90) cc_final: 0.8751 (t-170) REVERT: E 573 MET cc_start: 0.8825 (mmm) cc_final: 0.8461 (mmm) REVERT: E 590 GLU cc_start: 0.9583 (mp0) cc_final: 0.9304 (mp0) REVERT: E 613 ASP cc_start: 0.7804 (m-30) cc_final: 0.7453 (m-30) REVERT: E 680 MET cc_start: 0.9426 (ppp) cc_final: 0.9148 (ppp) REVERT: F 182 MET cc_start: 0.9278 (ttt) cc_final: 0.8562 (ppp) REVERT: F 236 MET cc_start: 0.9504 (mmp) cc_final: 0.9256 (mmm) REVERT: F 307 MET cc_start: 0.8948 (ppp) cc_final: 0.8462 (ppp) REVERT: F 456 LYS cc_start: 0.9257 (mttt) cc_final: 0.8744 (mttm) REVERT: F 548 MET cc_start: 0.9315 (mpp) cc_final: 0.8908 (ptm) REVERT: F 573 MET cc_start: 0.5625 (mtm) cc_final: 0.3893 (tmm) REVERT: F 585 MET cc_start: 0.8684 (tpt) cc_final: 0.7903 (tpt) REVERT: F 590 GLU cc_start: 0.9669 (mp0) cc_final: 0.9417 (mp0) REVERT: F 591 LEU cc_start: 0.9050 (tp) cc_final: 0.8620 (tp) REVERT: F 630 MET cc_start: 0.9380 (tpt) cc_final: 0.9179 (tpp) REVERT: F 717 PHE cc_start: 0.7673 (t80) cc_final: 0.7300 (t80) REVERT: G 524 VAL cc_start: 0.8605 (m) cc_final: 0.8227 (p) REVERT: G 570 MET cc_start: 0.8270 (ttt) cc_final: 0.7482 (ttt) REVERT: G 637 LEU cc_start: 0.8411 (mt) cc_final: 0.8046 (pt) REVERT: H 34 ILE cc_start: 0.8945 (pt) cc_final: 0.8610 (pt) REVERT: H 77 TYR cc_start: 0.7652 (t80) cc_final: 0.7296 (t80) REVERT: H 307 MET cc_start: 0.3813 (ptm) cc_final: 0.3503 (ppp) outliers start: 4 outliers final: 0 residues processed: 484 average time/residue: 0.2499 time to fit residues: 202.1021 Evaluate side-chains 379 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 148 optimal weight: 6.9990 chunk 376 optimal weight: 7.9990 chunk 531 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 559 optimal weight: 40.0000 chunk 279 optimal weight: 30.0000 chunk 249 optimal weight: 8.9990 chunk 519 optimal weight: 10.0000 chunk 582 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN C 30 GLN C 172 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 43 ASN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.078040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.061830 restraints weight = 492850.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.063053 restraints weight = 309633.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.063860 restraints weight = 217958.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.064541 restraints weight = 169429.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.065066 restraints weight = 137361.225| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46850 Z= 0.176 Angle : 0.720 13.037 63536 Z= 0.368 Chirality : 0.046 0.288 7315 Planarity : 0.005 0.083 8252 Dihedral : 5.247 34.686 6439 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.75 % 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: -1.38 (0.11), residues: 6053 helix: 0.04 (0.10), residues: 2860 sheet: -0.96 (0.17), residues: 895 loop : -2.05 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.020 0.002 TYR G 462 PHE 0.020 0.002 PHE B 463 TRP 0.028 0.002 TRP G 555 HIS 0.012 0.001 HIS C 564 Details of bonding type rmsd covalent geometry : bond 0.00367 (46850) covalent geometry : angle 0.71997 (63536) hydrogen bonds : bond 0.04000 ( 2081) hydrogen bonds : angle 4.93574 ( 6132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 462 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8008 (ptm) cc_final: 0.7471 (tmm) REVERT: A 69 ASN cc_start: 0.9318 (m-40) cc_final: 0.9079 (m-40) REVERT: A 182 MET cc_start: 0.9346 (ptp) cc_final: 0.8462 (tmm) REVERT: A 307 MET cc_start: 0.8323 (ppp) cc_final: 0.8072 (ppp) REVERT: A 396 LEU cc_start: 0.9136 (mm) cc_final: 0.8705 (tp) REVERT: A 507 MET cc_start: 0.7018 (mtp) cc_final: 0.6686 (ttt) REVERT: A 531 MET cc_start: 0.8218 (ttt) cc_final: 0.8013 (tpp) REVERT: A 548 MET cc_start: 0.2321 (mtt) cc_final: 0.2099 (mtt) REVERT: A 639 MET cc_start: 0.0592 (mmt) cc_final: -0.0453 (mmt) REVERT: A 641 MET cc_start: 0.6514 (ptt) cc_final: 0.5983 (ptt) REVERT: B 198 MET cc_start: 0.7781 (ptt) cc_final: 0.6776 (tpt) REVERT: B 307 MET cc_start: -0.0814 (ptt) cc_final: -0.3214 (tpt) REVERT: B 557 MET cc_start: 0.9588 (mmp) cc_final: 0.9383 (mmm) REVERT: B 630 MET cc_start: 0.8806 (tpt) cc_final: 0.8261 (tpp) REVERT: C 68 LYS cc_start: 0.9461 (pttp) cc_final: 0.9103 (pptt) REVERT: C 79 LYS cc_start: 0.9667 (tptt) cc_final: 0.9341 (mmmm) REVERT: C 98 MET cc_start: 0.8758 (mmp) cc_final: 0.8449 (mmp) REVERT: C 123 LYS cc_start: 0.9654 (mttt) cc_final: 0.9230 (mtpt) REVERT: C 182 MET cc_start: 0.9269 (ttt) cc_final: 0.8803 (ptp) REVERT: C 307 MET cc_start: 0.9659 (ptt) cc_final: 0.9300 (ppp) REVERT: C 394 ARG cc_start: 0.9334 (mtm180) cc_final: 0.8665 (ptt180) REVERT: C 557 MET cc_start: 0.9715 (mmp) cc_final: 0.9421 (mmm) REVERT: C 565 PHE cc_start: 0.9617 (p90) cc_final: 0.9401 (p90) REVERT: C 630 MET cc_start: 0.9703 (tpt) cc_final: 0.9298 (tpt) REVERT: C 823 ASP cc_start: 0.9478 (m-30) cc_final: 0.9143 (p0) REVERT: D 98 MET cc_start: 0.9043 (mmp) cc_final: 0.8723 (mmp) REVERT: D 182 MET cc_start: 0.9372 (ppp) cc_final: 0.9134 (ppp) REVERT: D 262 VAL cc_start: 0.9799 (t) cc_final: 0.9358 (t) REVERT: D 266 PHE cc_start: 0.9342 (m-80) cc_final: 0.9125 (m-80) REVERT: D 452 MET cc_start: 0.7349 (tpp) cc_final: 0.7017 (tpt) REVERT: D 483 LEU cc_start: 0.9392 (tp) cc_final: 0.9172 (tp) REVERT: D 580 TYR cc_start: 0.8546 (m-80) cc_final: 0.8274 (m-80) REVERT: D 582 PHE cc_start: 0.8195 (m-80) cc_final: 0.7724 (m-80) REVERT: D 618 LYS cc_start: 0.6894 (tttt) cc_final: 0.6493 (tttt) REVERT: D 630 MET cc_start: 0.9402 (mmp) cc_final: 0.9067 (mmm) REVERT: D 681 LEU cc_start: 0.9809 (mt) cc_final: 0.9559 (mt) REVERT: D 717 PHE cc_start: 0.6116 (t80) cc_final: 0.5299 (t80) REVERT: E 136 PHE cc_start: 0.9049 (m-80) cc_final: 0.8809 (m-10) REVERT: E 182 MET cc_start: 0.7525 (ppp) cc_final: 0.6786 (ppp) REVERT: E 266 PHE cc_start: 0.9540 (m-10) cc_final: 0.9253 (m-10) REVERT: E 307 MET cc_start: 0.8173 (ppp) cc_final: 0.7783 (ppp) REVERT: E 322 GLU cc_start: 0.7775 (tp30) cc_final: 0.7380 (mm-30) REVERT: E 360 MET cc_start: 0.9706 (mmm) cc_final: 0.9326 (mmm) REVERT: E 390 LEU cc_start: 0.8024 (mm) cc_final: 0.7653 (mm) REVERT: E 452 MET cc_start: 0.7133 (tpp) cc_final: 0.6737 (tpp) REVERT: E 548 MET cc_start: 0.9733 (ptp) cc_final: 0.9499 (mpp) REVERT: E 554 MET cc_start: 0.9278 (ppp) cc_final: 0.8620 (ptm) REVERT: E 564 HIS cc_start: 0.8993 (t-90) cc_final: 0.8696 (t-90) REVERT: E 573 MET cc_start: 0.8972 (mmm) cc_final: 0.8600 (mmm) REVERT: E 613 ASP cc_start: 0.7965 (m-30) cc_final: 0.7607 (m-30) REVERT: E 680 MET cc_start: 0.9349 (ppp) cc_final: 0.9048 (ppp) REVERT: F 182 MET cc_start: 0.9337 (ttt) cc_final: 0.8558 (ppp) REVERT: F 236 MET cc_start: 0.9428 (mmp) cc_final: 0.9205 (mmm) REVERT: F 307 MET cc_start: 0.9010 (ppp) cc_final: 0.8487 (ppp) REVERT: F 564 HIS cc_start: 0.9122 (t-90) cc_final: 0.8910 (m-70) REVERT: F 573 MET cc_start: 0.5552 (mtm) cc_final: 0.3723 (tmm) REVERT: F 585 MET cc_start: 0.8622 (tpt) cc_final: 0.7531 (tpt) REVERT: F 590 GLU cc_start: 0.9610 (mp0) cc_final: 0.9300 (mp0) REVERT: F 591 LEU cc_start: 0.9057 (tp) cc_final: 0.8673 (tp) REVERT: F 630 MET cc_start: 0.9443 (tpt) cc_final: 0.9197 (tpt) REVERT: F 680 MET cc_start: 0.9565 (ppp) cc_final: 0.9363 (ppp) REVERT: F 717 PHE cc_start: 0.7673 (t80) cc_final: 0.7306 (t80) REVERT: G 452 MET cc_start: 0.4670 (tmm) cc_final: 0.4379 (tmm) REVERT: G 524 VAL cc_start: 0.8859 (m) cc_final: 0.8200 (p) REVERT: G 570 MET cc_start: 0.8860 (ttt) cc_final: 0.8359 (ttt) REVERT: G 572 PHE cc_start: 0.8616 (m-10) cc_final: 0.8284 (m-80) REVERT: G 637 LEU cc_start: 0.8652 (mt) cc_final: 0.8363 (pt) REVERT: H 36 ARG cc_start: 0.8427 (tpt170) cc_final: 0.8041 (tpm170) REVERT: H 307 MET cc_start: 0.3773 (ptm) cc_final: 0.3411 (ppp) outliers start: 6 outliers final: 0 residues processed: 468 average time/residue: 0.2187 time to fit residues: 171.8055 Evaluate side-chains 365 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 583 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 410 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 466 optimal weight: 6.9990 chunk 274 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 30 GLN A 78 ASN A 132 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 636 ASN D 20 GLN D 30 GLN D 94 ASN D 132 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.079778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.063679 restraints weight = 482600.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.064810 restraints weight = 303577.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.065769 restraints weight = 215060.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.066408 restraints weight = 163592.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.066917 restraints weight = 136502.956| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46850 Z= 0.129 Angle : 0.701 12.742 63536 Z= 0.352 Chirality : 0.046 0.285 7315 Planarity : 0.005 0.076 8252 Dihedral : 5.021 33.501 6439 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.38 % 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: -1.17 (0.11), residues: 6053 helix: 0.25 (0.10), residues: 2847 sheet: -0.78 (0.18), residues: 826 loop : -2.01 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 283 TYR 0.017 0.001 TYR H 80 PHE 0.038 0.001 PHE C 35 TRP 0.022 0.001 TRP G 555 HIS 0.011 0.001 HIS E 70 Details of bonding type rmsd covalent geometry : bond 0.00284 (46850) covalent geometry : angle 0.70085 (63536) hydrogen bonds : bond 0.03807 ( 2081) hydrogen bonds : angle 4.79528 ( 6132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8030 (ptm) cc_final: 0.7494 (tmm) REVERT: A 69 ASN cc_start: 0.9305 (m-40) cc_final: 0.9060 (m-40) REVERT: A 182 MET cc_start: 0.9302 (ptp) cc_final: 0.8463 (tmm) REVERT: A 307 MET cc_start: 0.8225 (ppp) cc_final: 0.7976 (ppp) REVERT: A 396 LEU cc_start: 0.9072 (mm) cc_final: 0.8600 (tp) REVERT: A 507 MET cc_start: 0.7073 (mtp) cc_final: 0.6743 (ttt) REVERT: A 548 MET cc_start: 0.2092 (mtt) cc_final: 0.1884 (mtt) REVERT: B 84 LYS cc_start: 0.7686 (mmpt) cc_final: 0.7442 (tppt) REVERT: B 198 MET cc_start: 0.7743 (ptt) cc_final: 0.6701 (tpt) REVERT: B 307 MET cc_start: -0.0587 (ptt) cc_final: -0.2971 (tpt) REVERT: B 445 VAL cc_start: 0.9214 (t) cc_final: 0.8851 (p) REVERT: B 557 MET cc_start: 0.9587 (mmp) cc_final: 0.9369 (mmm) REVERT: B 590 GLU cc_start: 0.9219 (pm20) cc_final: 0.8904 (pm20) REVERT: B 630 MET cc_start: 0.8773 (tpt) cc_final: 0.8205 (tpp) REVERT: C 68 LYS cc_start: 0.9450 (pttp) cc_final: 0.9084 (pptt) REVERT: C 98 MET cc_start: 0.8850 (mmp) cc_final: 0.8631 (mmm) REVERT: C 123 LYS cc_start: 0.9579 (mttt) cc_final: 0.8874 (ptmt) REVERT: C 182 MET cc_start: 0.9205 (ttt) cc_final: 0.8799 (ptm) REVERT: C 236 MET cc_start: 0.9286 (ppp) cc_final: 0.9080 (ppp) REVERT: C 307 MET cc_start: 0.9649 (ptt) cc_final: 0.9309 (ppp) REVERT: C 394 ARG cc_start: 0.9307 (mtm180) cc_final: 0.8979 (mtm180) REVERT: C 554 MET cc_start: 0.9770 (mtt) cc_final: 0.9143 (mtt) REVERT: C 557 MET cc_start: 0.9684 (mmp) cc_final: 0.9310 (mmm) REVERT: C 565 PHE cc_start: 0.9548 (p90) cc_final: 0.9314 (p90) REVERT: C 585 MET cc_start: 0.6671 (mmt) cc_final: 0.5538 (mmm) REVERT: C 630 MET cc_start: 0.9719 (tpt) cc_final: 0.9472 (tpp) REVERT: D 98 MET cc_start: 0.9022 (mmp) cc_final: 0.8756 (mmp) REVERT: D 182 MET cc_start: 0.9349 (ppp) cc_final: 0.9077 (ppp) REVERT: D 262 VAL cc_start: 0.9800 (t) cc_final: 0.9326 (t) REVERT: D 266 PHE cc_start: 0.9296 (m-80) cc_final: 0.9078 (m-80) REVERT: D 452 MET cc_start: 0.7365 (tpp) cc_final: 0.7024 (tpt) REVERT: D 539 ILE cc_start: 0.9424 (mm) cc_final: 0.9187 (mp) REVERT: D 574 ASP cc_start: 0.8412 (p0) cc_final: 0.7731 (m-30) REVERT: D 580 TYR cc_start: 0.8516 (m-80) cc_final: 0.8222 (m-80) REVERT: D 582 PHE cc_start: 0.7978 (m-80) cc_final: 0.7510 (m-80) REVERT: D 618 LYS cc_start: 0.6502 (tttt) cc_final: 0.6073 (tttt) REVERT: D 630 MET cc_start: 0.9419 (mmp) cc_final: 0.9076 (mmm) REVERT: D 639 MET cc_start: 0.9068 (pmm) cc_final: 0.8854 (pmm) REVERT: D 681 LEU cc_start: 0.9821 (mt) cc_final: 0.9569 (pp) REVERT: D 717 PHE cc_start: 0.6083 (t80) cc_final: 0.5441 (t80) REVERT: D 774 TYR cc_start: 0.8695 (m-80) cc_final: 0.8035 (m-80) REVERT: E 70 HIS cc_start: 0.9356 (t-170) cc_final: 0.9141 (t-170) REVERT: E 136 PHE cc_start: 0.8989 (m-80) cc_final: 0.8755 (m-10) REVERT: E 182 MET cc_start: 0.7474 (ppp) cc_final: 0.6690 (ppp) REVERT: E 266 PHE cc_start: 0.9463 (m-10) cc_final: 0.9258 (m-10) REVERT: E 307 MET cc_start: 0.8005 (ppp) cc_final: 0.7577 (ppp) REVERT: E 322 GLU cc_start: 0.7901 (tp30) cc_final: 0.7509 (mm-30) REVERT: E 360 MET cc_start: 0.9683 (mmm) cc_final: 0.9309 (mmm) REVERT: E 390 LEU cc_start: 0.7953 (mm) cc_final: 0.7567 (mm) REVERT: E 452 MET cc_start: 0.7138 (tpp) cc_final: 0.6691 (tpp) REVERT: E 548 MET cc_start: 0.9689 (ptp) cc_final: 0.9477 (mpp) REVERT: E 554 MET cc_start: 0.9253 (ppp) cc_final: 0.8732 (ptm) REVERT: E 564 HIS cc_start: 0.9011 (t-90) cc_final: 0.8703 (t-90) REVERT: E 573 MET cc_start: 0.8914 (mmm) cc_final: 0.8524 (mmm) REVERT: E 590 GLU cc_start: 0.9536 (mp0) cc_final: 0.9288 (mp0) REVERT: E 613 ASP cc_start: 0.7888 (m-30) cc_final: 0.7570 (m-30) REVERT: E 680 MET cc_start: 0.9321 (ppp) cc_final: 0.8980 (ppp) REVERT: F 182 MET cc_start: 0.9279 (ttt) cc_final: 0.8553 (ppp) REVERT: F 236 MET cc_start: 0.9416 (mmp) cc_final: 0.9148 (mmm) REVERT: F 307 MET cc_start: 0.9057 (ppp) cc_final: 0.8645 (ppp) REVERT: F 342 LEU cc_start: 0.9403 (tp) cc_final: 0.9178 (tp) REVERT: F 573 MET cc_start: 0.5455 (mtm) cc_final: 0.3563 (tmm) REVERT: F 585 MET cc_start: 0.8328 (tpt) cc_final: 0.7294 (tpt) REVERT: F 630 MET cc_start: 0.9357 (tpt) cc_final: 0.9090 (tpp) REVERT: F 717 PHE cc_start: 0.7898 (t80) cc_final: 0.7583 (t80) REVERT: G 524 VAL cc_start: 0.8820 (m) cc_final: 0.8188 (p) REVERT: G 570 MET cc_start: 0.8741 (ttt) cc_final: 0.8159 (ttt) REVERT: G 637 LEU cc_start: 0.8581 (mt) cc_final: 0.8294 (pt) REVERT: H 307 MET cc_start: 0.4045 (ptm) cc_final: 0.3682 (ppp) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2353 time to fit residues: 188.7687 Evaluate side-chains 375 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 22 optimal weight: 30.0000 chunk 442 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 542 optimal weight: 7.9990 chunk 499 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN D 30 GLN D 94 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS D 560 HIS ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.078322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.062089 restraints weight = 488700.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.063415 restraints weight = 305552.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.064246 restraints weight = 215271.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.064995 restraints weight = 165920.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.065308 restraints weight = 135519.517| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 46850 Z= 0.147 Angle : 0.697 13.031 63536 Z= 0.354 Chirality : 0.046 0.282 7315 Planarity : 0.005 0.070 8252 Dihedral : 4.950 31.233 6439 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.38 % 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: -1.11 (0.11), residues: 6053 helix: 0.27 (0.10), residues: 2854 sheet: -0.72 (0.18), residues: 830 loop : -1.95 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 772 TYR 0.016 0.002 TYR H 80 PHE 0.031 0.002 PHE C 35 TRP 0.027 0.001 TRP G 555 HIS 0.008 0.001 HIS D 726 Details of bonding type rmsd covalent geometry : bond 0.00319 (46850) covalent geometry : angle 0.69725 (63536) hydrogen bonds : bond 0.03775 ( 2081) hydrogen bonds : angle 4.81994 ( 6132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 MET cc_start: 0.8037 (ptm) cc_final: 0.7619 (tmm) REVERT: A 69 ASN cc_start: 0.9346 (m-40) cc_final: 0.9116 (m-40) REVERT: A 307 MET cc_start: 0.8256 (ppp) cc_final: 0.8033 (ppp) REVERT: A 396 LEU cc_start: 0.9124 (mm) cc_final: 0.8650 (tp) REVERT: A 507 MET cc_start: 0.7208 (mtp) cc_final: 0.6893 (ttt) REVERT: A 641 MET cc_start: 0.7734 (ptt) cc_final: 0.7507 (ptt) REVERT: B 59 MET cc_start: 0.7678 (pmm) cc_final: 0.7189 (pmm) REVERT: B 84 LYS cc_start: 0.7679 (mmpt) cc_final: 0.7421 (tppt) REVERT: B 198 MET cc_start: 0.7965 (ptt) cc_final: 0.7085 (tpt) REVERT: B 307 MET cc_start: -0.0565 (ptt) cc_final: -0.2939 (tpt) REVERT: B 445 VAL cc_start: 0.9284 (t) cc_final: 0.8949 (p) REVERT: B 502 LEU cc_start: 0.9489 (pp) cc_final: 0.9221 (pp) REVERT: B 630 MET cc_start: 0.8848 (tpt) cc_final: 0.8367 (tpp) REVERT: C 68 LYS cc_start: 0.9475 (pttp) cc_final: 0.9143 (pptt) REVERT: C 98 MET cc_start: 0.9006 (mmp) cc_final: 0.8705 (mmp) REVERT: C 123 LYS cc_start: 0.9592 (mttt) cc_final: 0.9094 (mtpt) REVERT: C 182 MET cc_start: 0.9315 (ttt) cc_final: 0.8876 (ptp) REVERT: C 236 MET cc_start: 0.9396 (ppp) cc_final: 0.9185 (ppp) REVERT: C 307 MET cc_start: 0.9751 (ptt) cc_final: 0.9415 (ppp) REVERT: C 394 ARG cc_start: 0.9299 (mtm180) cc_final: 0.8803 (mtm180) REVERT: C 554 MET cc_start: 0.9765 (mtt) cc_final: 0.9186 (mtt) REVERT: C 557 MET cc_start: 0.9743 (mmp) cc_final: 0.9443 (mmm) REVERT: C 565 PHE cc_start: 0.9657 (p90) cc_final: 0.9408 (p90) REVERT: C 582 PHE cc_start: 0.9434 (m-80) cc_final: 0.9168 (m-80) REVERT: C 630 MET cc_start: 0.9742 (tpt) cc_final: 0.9376 (tpt) REVERT: D 182 MET cc_start: 0.9368 (ppp) cc_final: 0.9151 (ppp) REVERT: D 262 VAL cc_start: 0.9830 (t) cc_final: 0.9420 (t) REVERT: D 266 PHE cc_start: 0.9466 (m-80) cc_final: 0.9205 (m-80) REVERT: D 452 MET cc_start: 0.7475 (tpp) cc_final: 0.7232 (tpt) REVERT: D 582 PHE cc_start: 0.8077 (m-80) cc_final: 0.7572 (m-80) REVERT: D 618 LYS cc_start: 0.6882 (tttt) cc_final: 0.6502 (tttt) REVERT: D 630 MET cc_start: 0.9398 (mmp) cc_final: 0.9094 (mmm) REVERT: D 639 MET cc_start: 0.9183 (pmm) cc_final: 0.8917 (pmm) REVERT: D 681 LEU cc_start: 0.9853 (mt) cc_final: 0.9642 (mt) REVERT: D 717 PHE cc_start: 0.6245 (t80) cc_final: 0.5005 (t80) REVERT: D 824 PHE cc_start: 0.9207 (t80) cc_final: 0.9000 (t80) REVERT: E 70 HIS cc_start: 0.9421 (t-170) cc_final: 0.9213 (t70) REVERT: E 136 PHE cc_start: 0.9120 (m-80) cc_final: 0.8837 (m-10) REVERT: E 182 MET cc_start: 0.7525 (ppp) cc_final: 0.6860 (ppp) REVERT: E 307 MET cc_start: 0.8314 (ppp) cc_final: 0.7971 (ppp) REVERT: E 322 GLU cc_start: 0.8074 (tp30) cc_final: 0.7627 (mm-30) REVERT: E 360 MET cc_start: 0.9731 (mmm) cc_final: 0.9343 (mmm) REVERT: E 390 LEU cc_start: 0.8109 (mm) cc_final: 0.7773 (mm) REVERT: E 452 MET cc_start: 0.7237 (tpp) cc_final: 0.6782 (tpp) REVERT: E 564 HIS cc_start: 0.9076 (t-90) cc_final: 0.8761 (t-90) REVERT: E 573 MET cc_start: 0.8902 (mmm) cc_final: 0.8520 (mmm) REVERT: E 590 GLU cc_start: 0.9626 (mp0) cc_final: 0.9380 (mp0) REVERT: E 613 ASP cc_start: 0.7882 (m-30) cc_final: 0.7614 (m-30) REVERT: E 680 MET cc_start: 0.9441 (ppp) cc_final: 0.9086 (ppp) REVERT: F 182 MET cc_start: 0.9361 (ttt) cc_final: 0.8482 (tmm) REVERT: F 236 MET cc_start: 0.9511 (mmp) cc_final: 0.9232 (mmm) REVERT: F 307 MET cc_start: 0.9120 (ppp) cc_final: 0.8752 (ppp) REVERT: F 342 LEU cc_start: 0.9537 (tp) cc_final: 0.9270 (tp) REVERT: F 573 MET cc_start: 0.5287 (mtm) cc_final: 0.3411 (tmm) REVERT: F 585 MET cc_start: 0.8585 (tpt) cc_final: 0.7466 (tpt) REVERT: F 587 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8514 (pttm) REVERT: F 591 LEU cc_start: 0.9074 (tp) cc_final: 0.8594 (tp) REVERT: F 630 MET cc_start: 0.9427 (tpt) cc_final: 0.9200 (tpp) REVERT: F 680 MET cc_start: 0.9584 (ppp) cc_final: 0.9328 (ppp) REVERT: F 717 PHE cc_start: 0.8020 (t80) cc_final: 0.7662 (t80) REVERT: F 724 MET cc_start: 0.9329 (tpt) cc_final: 0.8989 (tpp) REVERT: G 452 MET cc_start: 0.5040 (tmm) cc_final: 0.4840 (tmm) REVERT: G 524 VAL cc_start: 0.8740 (m) cc_final: 0.8000 (p) REVERT: G 637 LEU cc_start: 0.8490 (mt) cc_final: 0.8208 (pt) REVERT: H 307 MET cc_start: 0.4026 (ptm) cc_final: 0.3659 (ppp) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1842 time to fit residues: 142.0703 Evaluate side-chains 364 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 52 optimal weight: 40.0000 chunk 554 optimal weight: 5.9990 chunk 447 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 539 optimal weight: 0.9980 chunk 565 optimal weight: 10.0000 chunk 575 optimal weight: 40.0000 chunk 377 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 145 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.076406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.060220 restraints weight = 493840.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.061435 restraints weight = 313303.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.062197 restraints weight = 222372.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.062915 restraints weight = 172875.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.063384 restraints weight = 139824.926| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 46850 Z= 0.177 Angle : 0.723 13.266 63536 Z= 0.369 Chirality : 0.046 0.299 7315 Planarity : 0.005 0.074 8252 Dihedral : 5.021 30.037 6439 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.38 % 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 (0.11), residues: 6053 helix: 0.19 (0.10), residues: 2867 sheet: -0.72 (0.18), residues: 828 loop : -2.03 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 384 TYR 0.025 0.002 TYR H 77 PHE 0.028 0.002 PHE C 35 TRP 0.027 0.002 TRP G 555 HIS 0.008 0.001 HIS D 726 Details of bonding type rmsd covalent geometry : bond 0.00376 (46850) covalent geometry : angle 0.72257 (63536) hydrogen bonds : bond 0.03859 ( 2081) hydrogen bonds : angle 4.93481 ( 6132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8101 (ptm) cc_final: 0.7668 (tmm) REVERT: A 69 ASN cc_start: 0.9351 (m-40) cc_final: 0.9132 (m-40) REVERT: A 182 MET cc_start: 0.9230 (ptp) cc_final: 0.8115 (tmm) REVERT: A 396 LEU cc_start: 0.9184 (mm) cc_final: 0.8751 (tp) REVERT: A 507 MET cc_start: 0.7149 (mtp) cc_final: 0.6854 (ttt) REVERT: A 641 MET cc_start: 0.7356 (ptt) cc_final: 0.7050 (ptt) REVERT: B 84 LYS cc_start: 0.7533 (mmpt) cc_final: 0.7283 (tppt) REVERT: B 198 MET cc_start: 0.6806 (ptm) cc_final: 0.6429 (tpt) REVERT: B 236 MET cc_start: 0.8011 (mpp) cc_final: 0.7759 (mpp) REVERT: B 307 MET cc_start: -0.0913 (ptt) cc_final: -0.3327 (tpt) REVERT: B 445 VAL cc_start: 0.9318 (t) cc_final: 0.9009 (p) REVERT: B 452 MET cc_start: 0.7668 (mmp) cc_final: 0.5132 (tpt) REVERT: B 502 LEU cc_start: 0.9516 (pp) cc_final: 0.9108 (pp) REVERT: B 630 MET cc_start: 0.8910 (tpt) cc_final: 0.8498 (tpt) REVERT: C 68 LYS cc_start: 0.9424 (pttp) cc_final: 0.9070 (pptt) REVERT: C 98 MET cc_start: 0.8946 (mmp) cc_final: 0.8609 (mmp) REVERT: C 123 LYS cc_start: 0.9615 (mttt) cc_final: 0.9151 (mtpt) REVERT: C 182 MET cc_start: 0.9266 (ttt) cc_final: 0.8938 (ptm) REVERT: C 236 MET cc_start: 0.9336 (ppp) cc_final: 0.9134 (ppp) REVERT: C 307 MET cc_start: 0.9678 (ptt) cc_final: 0.9365 (ppp) REVERT: C 394 ARG cc_start: 0.9253 (mtm180) cc_final: 0.8733 (mtm180) REVERT: C 476 GLU cc_start: 0.9355 (pm20) cc_final: 0.9149 (pm20) REVERT: C 557 MET cc_start: 0.9716 (mmp) cc_final: 0.9424 (mmm) REVERT: C 565 PHE cc_start: 0.9594 (p90) cc_final: 0.9337 (p90) REVERT: C 630 MET cc_start: 0.9720 (tpt) cc_final: 0.9349 (tpp) REVERT: D 98 MET cc_start: 0.9033 (mmp) cc_final: 0.8789 (mmp) REVERT: D 182 MET cc_start: 0.9365 (ppp) cc_final: 0.9116 (ppp) REVERT: D 262 VAL cc_start: 0.9803 (t) cc_final: 0.9366 (t) REVERT: D 452 MET cc_start: 0.7890 (tpp) cc_final: 0.7671 (tpt) REVERT: D 483 LEU cc_start: 0.9461 (tp) cc_final: 0.9218 (tp) REVERT: D 518 ASP cc_start: 0.9010 (p0) cc_final: 0.8716 (t0) REVERT: D 582 PHE cc_start: 0.8087 (m-80) cc_final: 0.7585 (m-80) REVERT: D 618 LYS cc_start: 0.7085 (tttt) cc_final: 0.6753 (tttt) REVERT: D 630 MET cc_start: 0.9457 (mmp) cc_final: 0.9108 (mmm) REVERT: D 639 MET cc_start: 0.9211 (pmm) cc_final: 0.8942 (pmm) REVERT: D 681 LEU cc_start: 0.9828 (mt) cc_final: 0.9599 (mt) REVERT: D 717 PHE cc_start: 0.6303 (t80) cc_final: 0.5466 (t80) REVERT: E 136 PHE cc_start: 0.9063 (m-80) cc_final: 0.8809 (m-10) REVERT: E 182 MET cc_start: 0.7753 (ppp) cc_final: 0.6989 (ppp) REVERT: E 266 PHE cc_start: 0.9530 (m-80) cc_final: 0.9159 (m-10) REVERT: E 307 MET cc_start: 0.8306 (ppp) cc_final: 0.8033 (ppp) REVERT: E 322 GLU cc_start: 0.8117 (tp30) cc_final: 0.7727 (mm-30) REVERT: E 360 MET cc_start: 0.9715 (mmm) cc_final: 0.9317 (mmm) REVERT: E 390 LEU cc_start: 0.8327 (mm) cc_final: 0.7931 (mm) REVERT: E 452 MET cc_start: 0.7384 (tpp) cc_final: 0.6897 (tpp) REVERT: E 554 MET cc_start: 0.9426 (ptm) cc_final: 0.9175 (ptm) REVERT: E 564 HIS cc_start: 0.9019 (t-90) cc_final: 0.8671 (t-90) REVERT: E 573 MET cc_start: 0.8940 (mmm) cc_final: 0.8585 (mmm) REVERT: E 590 GLU cc_start: 0.9525 (mp0) cc_final: 0.9269 (mp0) REVERT: E 613 ASP cc_start: 0.8057 (m-30) cc_final: 0.7797 (m-30) REVERT: E 680 MET cc_start: 0.9152 (ppp) cc_final: 0.8944 (ppp) REVERT: F 182 MET cc_start: 0.9380 (ttt) cc_final: 0.8458 (tmm) REVERT: F 236 MET cc_start: 0.9433 (mmp) cc_final: 0.9176 (mmm) REVERT: F 307 MET cc_start: 0.9142 (ppp) cc_final: 0.8736 (ppp) REVERT: F 573 MET cc_start: 0.5194 (mtm) cc_final: 0.3298 (tmm) REVERT: F 585 MET cc_start: 0.8415 (tpt) cc_final: 0.7298 (tpt) REVERT: F 587 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8644 (pttm) REVERT: F 717 PHE cc_start: 0.7982 (t80) cc_final: 0.7614 (t80) REVERT: F 724 MET cc_start: 0.9377 (tpt) cc_final: 0.9033 (tpp) REVERT: G 452 MET cc_start: 0.5037 (tmm) cc_final: 0.4637 (tmm) REVERT: G 524 VAL cc_start: 0.8959 (m) cc_final: 0.8286 (p) REVERT: G 570 MET cc_start: 0.9027 (ttt) cc_final: 0.8750 (ttt) REVERT: G 637 LEU cc_start: 0.8723 (mt) cc_final: 0.8382 (pt) REVERT: H 307 MET cc_start: 0.3731 (ptm) cc_final: 0.3365 (ppp) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1683 time to fit residues: 126.3535 Evaluate side-chains 349 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 21 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 213 optimal weight: 20.0000 chunk 423 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 296 optimal weight: 6.9990 chunk 537 optimal weight: 4.9990 chunk 508 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 691 ASN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.076678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.060775 restraints weight = 493521.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.061973 restraints weight = 305771.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062746 restraints weight = 215838.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.063515 restraints weight = 166272.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.063866 restraints weight = 134390.252| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46850 Z= 0.149 Angle : 0.711 12.384 63536 Z= 0.360 Chirality : 0.046 0.284 7315 Planarity : 0.005 0.072 8252 Dihedral : 4.945 29.384 6439 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.16 (0.11), residues: 6053 helix: 0.23 (0.10), residues: 2869 sheet: -0.69 (0.18), residues: 822 loop : -2.03 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 578 TYR 0.028 0.002 TYR B 203 PHE 0.025 0.002 PHE H 345 TRP 0.027 0.002 TRP G 555 HIS 0.011 0.001 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00324 (46850) covalent geometry : angle 0.71137 (63536) hydrogen bonds : bond 0.03699 ( 2081) hydrogen bonds : angle 4.86873 ( 6132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8214 (ptm) cc_final: 0.7678 (tmm) REVERT: A 69 ASN cc_start: 0.9410 (m-40) cc_final: 0.9190 (m-40) REVERT: A 80 TYR cc_start: 0.8581 (m-80) cc_final: 0.8171 (m-80) REVERT: A 182 MET cc_start: 0.9259 (ptp) cc_final: 0.8954 (ppp) REVERT: A 396 LEU cc_start: 0.9216 (mm) cc_final: 0.8750 (tp) REVERT: A 452 MET cc_start: 0.2436 (tpt) cc_final: 0.2171 (tpt) REVERT: A 548 MET cc_start: 0.4066 (mtt) cc_final: 0.3671 (mtt) REVERT: A 641 MET cc_start: 0.7661 (ptt) cc_final: 0.7391 (ptt) REVERT: B 84 LYS cc_start: 0.7497 (mmpt) cc_final: 0.7252 (tppt) REVERT: B 307 MET cc_start: -0.0839 (ptt) cc_final: -0.3249 (tpt) REVERT: B 445 VAL cc_start: 0.9318 (t) cc_final: 0.8996 (p) REVERT: B 452 MET cc_start: 0.7872 (mmp) cc_final: 0.6598 (tpp) REVERT: B 502 LEU cc_start: 0.9418 (pp) cc_final: 0.9096 (pp) REVERT: B 630 MET cc_start: 0.8972 (tpt) cc_final: 0.8535 (tpt) REVERT: C 65 LYS cc_start: 0.9539 (mtpt) cc_final: 0.9164 (mttt) REVERT: C 98 MET cc_start: 0.9087 (mmp) cc_final: 0.8789 (mmp) REVERT: C 123 LYS cc_start: 0.9660 (mttt) cc_final: 0.9241 (mtpt) REVERT: C 182 MET cc_start: 0.9337 (ttt) cc_final: 0.8967 (ptp) REVERT: C 236 MET cc_start: 0.9401 (ppp) cc_final: 0.9185 (ppp) REVERT: C 307 MET cc_start: 0.9754 (ptt) cc_final: 0.9451 (ppp) REVERT: C 394 ARG cc_start: 0.9295 (mtm180) cc_final: 0.8780 (mtm180) REVERT: C 476 GLU cc_start: 0.9485 (pm20) cc_final: 0.9283 (pm20) REVERT: C 539 ILE cc_start: 0.9737 (mm) cc_final: 0.9479 (mp) REVERT: C 557 MET cc_start: 0.9770 (mmp) cc_final: 0.9484 (mmm) REVERT: C 565 PHE cc_start: 0.9674 (p90) cc_final: 0.9391 (p90) REVERT: C 630 MET cc_start: 0.9745 (tpt) cc_final: 0.9468 (tpp) REVERT: D 52 MET cc_start: 0.9199 (ppp) cc_final: 0.8605 (ppp) REVERT: D 182 MET cc_start: 0.9371 (ppp) cc_final: 0.9147 (ppp) REVERT: D 262 VAL cc_start: 0.9828 (t) cc_final: 0.9474 (t) REVERT: D 518 ASP cc_start: 0.9063 (p0) cc_final: 0.8808 (t0) REVERT: D 582 PHE cc_start: 0.8003 (m-80) cc_final: 0.7524 (m-80) REVERT: D 618 LYS cc_start: 0.7437 (tttt) cc_final: 0.7187 (tttt) REVERT: D 630 MET cc_start: 0.9377 (mmp) cc_final: 0.9079 (mmm) REVERT: D 717 PHE cc_start: 0.6509 (t80) cc_final: 0.5292 (t80) REVERT: E 136 PHE cc_start: 0.9200 (m-80) cc_final: 0.8927 (m-10) REVERT: E 182 MET cc_start: 0.7719 (ppp) cc_final: 0.6913 (ppp) REVERT: E 322 GLU cc_start: 0.8159 (tp30) cc_final: 0.7715 (mm-30) REVERT: E 360 MET cc_start: 0.9751 (mmm) cc_final: 0.9359 (mmm) REVERT: E 390 LEU cc_start: 0.8296 (mm) cc_final: 0.7894 (mm) REVERT: E 452 MET cc_start: 0.7410 (tpp) cc_final: 0.6910 (tpp) REVERT: E 554 MET cc_start: 0.9505 (ptm) cc_final: 0.9272 (ptm) REVERT: E 564 HIS cc_start: 0.8960 (t-90) cc_final: 0.8669 (t-170) REVERT: E 573 MET cc_start: 0.8934 (mmm) cc_final: 0.8558 (mmm) REVERT: E 590 GLU cc_start: 0.9628 (mp0) cc_final: 0.9330 (mp0) REVERT: E 613 ASP cc_start: 0.8034 (m-30) cc_final: 0.7825 (m-30) REVERT: E 680 MET cc_start: 0.9311 (ppp) cc_final: 0.9092 (ppp) REVERT: F 182 MET cc_start: 0.9473 (ttt) cc_final: 0.8667 (tmm) REVERT: F 236 MET cc_start: 0.9525 (mmp) cc_final: 0.9296 (mmp) REVERT: F 238 LYS cc_start: 0.9765 (pttt) cc_final: 0.9531 (ptpp) REVERT: F 307 MET cc_start: 0.9146 (ppp) cc_final: 0.8773 (ppp) REVERT: F 573 MET cc_start: 0.5034 (mtm) cc_final: 0.3132 (tmm) REVERT: F 585 MET cc_start: 0.8610 (tpt) cc_final: 0.7666 (tpt) REVERT: F 587 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8477 (pttm) REVERT: F 591 LEU cc_start: 0.9149 (tp) cc_final: 0.8639 (tp) REVERT: F 630 MET cc_start: 0.9451 (tpt) cc_final: 0.9227 (tpp) REVERT: F 680 MET cc_start: 0.9608 (ppp) cc_final: 0.9364 (ppp) REVERT: F 717 PHE cc_start: 0.7931 (t80) cc_final: 0.7611 (t80) REVERT: F 724 MET cc_start: 0.9411 (tpt) cc_final: 0.9086 (tpp) REVERT: G 452 MET cc_start: 0.5502 (tmm) cc_final: 0.5221 (tmm) REVERT: G 524 VAL cc_start: 0.8828 (m) cc_final: 0.8165 (p) REVERT: G 570 MET cc_start: 0.8834 (ttt) cc_final: 0.8515 (ttt) REVERT: G 637 LEU cc_start: 0.8563 (mt) cc_final: 0.8357 (pt) REVERT: H 307 MET cc_start: 0.3837 (ptm) cc_final: 0.3479 (ppp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1693 time to fit residues: 127.8784 Evaluate side-chains 361 residues out of total 4809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 42 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 344 optimal weight: 40.0000 chunk 324 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 341 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 HIS C 815 GLN D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN D 751 ASN ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 691 ASN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.058724 restraints weight = 498538.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060146 restraints weight = 313262.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.060648 restraints weight = 211651.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.061962 restraints weight = 158449.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.061670 restraints weight = 132493.908| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46850 Z= 0.189 Angle : 0.744 12.218 63536 Z= 0.381 Chirality : 0.046 0.288 7315 Planarity : 0.005 0.085 8252 Dihedral : 5.075 27.675 6439 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.25 (0.11), residues: 6053 helix: 0.13 (0.10), residues: 2871 sheet: -0.64 (0.18), residues: 816 loop : -2.07 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 480 TYR 0.021 0.002 TYR E 462 PHE 0.034 0.002 PHE E 463 TRP 0.031 0.002 TRP G 555 HIS 0.008 0.001 HIS E 70 Details of bonding type rmsd covalent geometry : bond 0.00397 (46850) covalent geometry : angle 0.74357 (63536) hydrogen bonds : bond 0.03884 ( 2081) hydrogen bonds : angle 4.98389 ( 6132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8985.28 seconds wall clock time: 156 minutes 10.74 seconds (9370.74 seconds total)