Starting phenix.real_space_refine on Mon Jul 6 13:26:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.map" model { file = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lmy_23442/07_2026/7lmy_23442.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 22338 2.51 5 N 6300 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35646 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.46, per 1000 atoms: 0.21 Number of scatterers: 35646 At special positions: 0 Unit cell: (175.395, 169.017, 113.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6768 8.00 N 6300 7.00 C 22338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 30 sheets defined 53.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.071A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.529A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.020A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 4.191A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.071A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.512A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.744A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.529A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 612 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.910A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.558A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 612 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.910A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.073A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.776A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.744A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 removed outlier: 3.815A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.511A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.020A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 612 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.507A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 14 through 18 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.776A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.512A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 612 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.600A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.470A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.471A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.479A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.471A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.479A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 4716 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: 9.69 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12156 1.35 - 1.47: 7157 1.47 - 1.59: 16602 1.59 - 1.71: 37 1.71 - 1.83: 300 Bond restraints: 36252 Sorted by residual: bond pdb=" C10 Y6Y A 903 " pdb=" S Y6Y A 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C10 Y6Y B 903 " pdb=" S Y6Y B 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C10 Y6Y F 903 " pdb=" S Y6Y F 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C10 Y6Y D 903 " pdb=" S Y6Y D 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C10 Y6Y E 903 " pdb=" S Y6Y E 903 " ideal model delta sigma weight residual 1.774 1.595 0.179 2.00e-02 2.50e+03 8.04e+01 ... (remaining 36247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 48628 3.32 - 6.64: 326 6.64 - 9.96: 60 9.96 - 13.28: 6 13.28 - 16.60: 12 Bond angle restraints: 49032 Sorted by residual: angle pdb=" CB ARG C 225 " pdb=" CG ARG C 225 " pdb=" CD ARG C 225 " ideal model delta sigma weight residual 111.30 126.26 -14.96 2.30e+00 1.89e-01 4.23e+01 angle pdb=" CB ARG B 225 " pdb=" CG ARG B 225 " pdb=" CD ARG B 225 " ideal model delta sigma weight residual 111.30 126.24 -14.94 2.30e+00 1.89e-01 4.22e+01 angle pdb=" CB ARG D 225 " pdb=" CG ARG D 225 " pdb=" CD ARG D 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG E 225 " pdb=" CG ARG E 225 " pdb=" CD ARG E 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG F 225 " pdb=" CG ARG F 225 " pdb=" CD ARG F 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 ... (remaining 49027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20383 17.86 - 35.72: 1479 35.72 - 53.57: 290 53.57 - 71.43: 96 71.43 - 89.29: 60 Dihedral angle restraints: 22308 sinusoidal: 9426 harmonic: 12882 Sorted by residual: dihedral pdb=" CA GLN C 19 " pdb=" C GLN C 19 " pdb=" N LYS C 20 " pdb=" CA LYS C 20 " ideal model delta harmonic sigma weight residual 180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN A 19 " pdb=" C GLN A 19 " pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN B 19 " pdb=" C GLN B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 22305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4407 0.053 - 0.106: 887 0.106 - 0.158: 172 0.158 - 0.211: 6 0.211 - 0.264: 6 Chirality restraints: 5478 Sorted by residual: chirality pdb=" C17 Y6Y A 903 " pdb=" C18 Y6Y A 903 " pdb=" C21 Y6Y A 903 " pdb=" S1 Y6Y A 903 " both_signs ideal model delta sigma weight residual False 3.51 3.24 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C17 Y6Y F 903 " pdb=" C18 Y6Y F 903 " pdb=" C21 Y6Y F 903 " pdb=" S1 Y6Y F 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C17 Y6Y B 903 " pdb=" C18 Y6Y B 903 " pdb=" C21 Y6Y B 903 " pdb=" S1 Y6Y B 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5475 not shown) Planarity restraints: 6390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 237 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO D 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 237 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 238 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 237 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.88e+01 pdb=" N PRO C 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.058 5.00e-02 4.00e+02 ... (remaining 6387 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 288 2.57 - 3.15: 28581 3.15 - 3.73: 56756 3.73 - 4.32: 81802 4.32 - 4.90: 130818 Nonbonded interactions: 298245 Sorted by model distance: nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 904 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 904 " model vdw 1.996 2.170 nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 904 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 904 " model vdw 2.011 2.170 ... (remaining 298240 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: 0.13 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.070 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 36252 Z= 0.233 Angle : 0.769 16.598 49032 Z= 0.395 Chirality : 0.045 0.264 5478 Planarity : 0.005 0.109 6390 Dihedral : 14.250 89.289 13944 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.89 % Allowed : 0.47 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4434 helix: 0.96 (0.12), residues: 1962 sheet: 0.52 (0.20), residues: 654 loop : 0.53 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 711 TYR 0.011 0.001 TYR C 203 PHE 0.018 0.001 PHE C 742 TRP 0.005 0.001 TRP D 454 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (36252) covalent geometry : angle 0.76947 / 0.39 (49032) hydrogen bonds : bond 0.15776 / 10.40 ( 1683) hydrogen bonds : angle 5.62685 / 3.96 ( 4716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 427 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6588 (mmm) outliers start: 72 outliers final: 5 residues processed: 283 average time/residue: 1.1364 time to fit residues: 364.7010 Evaluate side-chains 150 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain F residue 427 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.0970 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS B 115 HIS B 406 HIS C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 226 HIS E 115 HIS E 406 HIS F 115 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059476 restraints weight = 75685.547| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.83 r_work: 0.2810 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36252 Z= 0.135 Angle : 0.558 6.535 49032 Z= 0.292 Chirality : 0.044 0.163 5478 Planarity : 0.005 0.081 6390 Dihedral : 6.743 58.779 5010 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.60 % Allowed : 6.18 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.13), residues: 4434 helix: 1.21 (0.11), residues: 2034 sheet: 0.75 (0.20), residues: 624 loop : 0.87 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 713 TYR 0.007 0.001 TYR F 755 PHE 0.009 0.001 PHE B 563 TRP 0.006 0.001 TRP D 454 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (36252) covalent geometry : angle 0.55790 / 0.29 (49032) hydrogen bonds : bond 0.04048 / 2.67 ( 1683) hydrogen bonds : angle 4.44735 / 3.12 ( 4716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ASN cc_start: 0.8930 (m-40) cc_final: 0.8534 (p0) REVERT: C 158 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6909 (pp-130) outliers start: 23 outliers final: 6 residues processed: 147 average time/residue: 0.8044 time to fit residues: 140.9079 Evaluate side-chains 138 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 305 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 0.4980 chunk 441 optimal weight: 6.9990 chunk 394 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS B 115 HIS B 183 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 183 HIS E 115 HIS E 183 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 183 HIS F 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.057638 restraints weight = 75689.382| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.79 r_work: 0.2773 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36252 Z= 0.157 Angle : 0.518 7.642 49032 Z= 0.271 Chirality : 0.044 0.155 5478 Planarity : 0.004 0.070 6390 Dihedral : 6.655 59.999 4992 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.00 % Allowed : 6.70 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4434 helix: 1.35 (0.12), residues: 2046 sheet: 0.76 (0.20), residues: 624 loop : 1.00 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 93 TYR 0.016 0.001 TYR C 138 PHE 0.009 0.001 PHE A 139 TRP 0.006 0.001 TRP D 454 HIS 0.011 0.002 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (36252) covalent geometry : angle 0.51801 / 0.27 (49032) hydrogen bonds : bond 0.04051 / 2.69 ( 1683) hydrogen bonds : angle 4.29274 / 3.02 ( 4716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6364 (mpt) cc_final: 0.6159 (mpt) REVERT: B 199 ASN cc_start: 0.8927 (m110) cc_final: 0.8533 (p0) REVERT: C 158 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6705 (pp-130) REVERT: F 158 MET cc_start: 0.7112 (pmm) cc_final: 0.6890 (ppp) outliers start: 38 outliers final: 13 residues processed: 160 average time/residue: 0.7049 time to fit residues: 136.1477 Evaluate side-chains 145 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 15 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 330 optimal weight: 0.0980 chunk 293 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055916 restraints weight = 76129.582| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.77 r_work: 0.2734 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36252 Z= 0.212 Angle : 0.530 7.365 49032 Z= 0.276 Chirality : 0.045 0.151 5478 Planarity : 0.004 0.064 6390 Dihedral : 6.662 59.967 4992 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.50 % Allowed : 7.65 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.13), residues: 4434 helix: 1.34 (0.11), residues: 2076 sheet: 0.76 (0.20), residues: 624 loop : 1.08 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 93 TYR 0.015 0.001 TYR F 138 PHE 0.010 0.002 PHE A 302 TRP 0.007 0.001 TRP D 454 HIS 0.011 0.002 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (36252) covalent geometry : angle 0.53016 / 0.28 (49032) hydrogen bonds : bond 0.04168 / 2.76 ( 1683) hydrogen bonds : angle 4.25845 / 3.01 ( 4716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.458 Fit side-chains REVERT: A 46 MET cc_start: 0.6289 (mpt) cc_final: 0.6051 (mpt) REVERT: A 158 MET cc_start: 0.7493 (pmm) cc_final: 0.7215 (ppp) REVERT: B 158 MET cc_start: 0.7455 (pmm) cc_final: 0.7142 (ppp) REVERT: B 199 ASN cc_start: 0.8928 (m110) cc_final: 0.8536 (p0) REVERT: B 508 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8802 (tmm) REVERT: C 46 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6713 (mpp) REVERT: C 158 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7059 (pp-130) REVERT: E 158 MET cc_start: 0.7474 (pmm) cc_final: 0.7233 (ppp) REVERT: E 508 MET cc_start: 0.9069 (ttt) cc_final: 0.8855 (tmm) REVERT: F 158 MET cc_start: 0.7282 (pmm) cc_final: 0.7067 (ppp) outliers start: 19 outliers final: 8 residues processed: 144 average time/residue: 0.7168 time to fit residues: 124.5277 Evaluate side-chains 139 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 22 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 374 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056056 restraints weight = 75732.264| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.80 r_work: 0.2738 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36252 Z= 0.159 Angle : 0.488 7.207 49032 Z= 0.254 Chirality : 0.043 0.153 5478 Planarity : 0.004 0.058 6390 Dihedral : 6.214 56.427 4992 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.55 % Allowed : 8.20 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.13), residues: 4434 helix: 1.43 (0.11), residues: 2082 sheet: 0.74 (0.21), residues: 624 loop : 1.07 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 86 TYR 0.011 0.001 TYR F 138 PHE 0.011 0.001 PHE C 152 TRP 0.007 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (36252) covalent geometry : angle 0.48765 / 0.25 (49032) hydrogen bonds : bond 0.03688 / 2.43 ( 1683) hydrogen bonds : angle 4.11483 / 2.91 ( 4716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.466 Fit side-chains REVERT: A 46 MET cc_start: 0.6345 (mpt) cc_final: 0.6096 (mpt) REVERT: B 158 MET cc_start: 0.7577 (pmm) cc_final: 0.7343 (ppp) REVERT: B 199 ASN cc_start: 0.8913 (m110) cc_final: 0.8508 (p0) REVERT: B 508 MET cc_start: 0.9057 (ttt) cc_final: 0.8802 (tmm) REVERT: C 46 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6714 (mtp) REVERT: C 158 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7093 (ppp) REVERT: D 219 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9054 (mtm) REVERT: E 199 ASN cc_start: 0.8964 (m-40) cc_final: 0.8532 (p0) REVERT: E 508 MET cc_start: 0.9106 (ttt) cc_final: 0.8805 (tmm) outliers start: 21 outliers final: 8 residues processed: 140 average time/residue: 0.6704 time to fit residues: 113.2068 Evaluate side-chains 136 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 324 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 109 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 115 HIS ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 337 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 = 0.3764 r_free = 0.3764 target = 0.096406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.055958 restraints weight = 75628.427| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.80 r_work: 0.2736 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36252 Z= 0.154 Angle : 0.488 8.648 49032 Z= 0.253 Chirality : 0.043 0.153 5478 Planarity : 0.004 0.056 6390 Dihedral : 5.903 53.200 4992 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.76 % Allowed : 8.25 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.13), residues: 4434 helix: 1.50 (0.11), residues: 2082 sheet: 0.77 (0.21), residues: 624 loop : 1.09 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 93 TYR 0.025 0.001 TYR B 173 PHE 0.009 0.001 PHE D 302 TRP 0.007 0.001 TRP D 454 HIS 0.014 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (36252) covalent geometry : angle 0.48759 / 0.25 (49032) hydrogen bonds : bond 0.03685 / 2.45 ( 1683) hydrogen bonds : angle 4.09926 / 2.90 ( 4716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.481 Fit side-chains REVERT: A 46 MET cc_start: 0.6395 (mpt) cc_final: 0.6125 (mpt) REVERT: A 158 MET cc_start: 0.7324 (pmm) cc_final: 0.7054 (ppp) REVERT: B 158 MET cc_start: 0.7643 (pmm) cc_final: 0.7202 (pp-130) REVERT: B 199 ASN cc_start: 0.8903 (m110) cc_final: 0.8484 (p0) REVERT: B 508 MET cc_start: 0.9076 (ttt) cc_final: 0.8796 (tmm) REVERT: C 46 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: C 158 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7324 (ppp) REVERT: E 199 ASN cc_start: 0.8963 (m-40) cc_final: 0.8531 (p0) REVERT: E 508 MET cc_start: 0.9107 (ttt) cc_final: 0.8788 (tmm) REVERT: E 701 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8529 (tt0) outliers start: 29 outliers final: 10 residues processed: 148 average time/residue: 0.7609 time to fit residues: 134.7813 Evaluate side-chains 139 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 353 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 375 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.096045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055406 restraints weight = 76283.953| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.79 r_work: 0.2730 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36252 Z= 0.178 Angle : 0.505 9.123 49032 Z= 0.260 Chirality : 0.044 0.149 5478 Planarity : 0.004 0.055 6390 Dihedral : 5.662 50.100 4992 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.84 % Allowed : 8.49 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.13), residues: 4434 helix: 1.50 (0.11), residues: 2082 sheet: 0.50 (0.20), residues: 666 loop : 1.15 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 599 TYR 0.022 0.001 TYR E 173 PHE 0.009 0.001 PHE C 152 TRP 0.007 0.001 TRP D 454 HIS 0.014 0.002 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (36252) covalent geometry : angle 0.50501 / 0.26 (49032) hydrogen bonds : bond 0.03795 / 2.51 ( 1683) hydrogen bonds : angle 4.10956 / 2.91 ( 4716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6426 (mpt) cc_final: 0.6151 (mpt) REVERT: A 225 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (mmm-85) REVERT: B 158 MET cc_start: 0.7600 (pmm) cc_final: 0.7147 (pp-130) REVERT: B 199 ASN cc_start: 0.8914 (m110) cc_final: 0.8491 (p0) REVERT: B 508 MET cc_start: 0.9102 (ttt) cc_final: 0.8821 (tmm) REVERT: B 701 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: C 46 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6743 (mtp) REVERT: C 158 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7227 (ppp) REVERT: C 199 ASN cc_start: 0.8936 (m-40) cc_final: 0.8569 (p0) REVERT: E 158 MET cc_start: 0.7535 (pmm) cc_final: 0.7149 (ppp) REVERT: E 199 ASN cc_start: 0.8969 (m-40) cc_final: 0.8519 (p0) REVERT: E 508 MET cc_start: 0.9133 (ttt) cc_final: 0.8794 (tmm) REVERT: E 701 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: F 158 MET cc_start: 0.7429 (pmm) cc_final: 0.7195 (ppp) REVERT: F 199 ASN cc_start: 0.8951 (m-40) cc_final: 0.8559 (p0) outliers start: 32 outliers final: 10 residues processed: 154 average time/residue: 0.7695 time to fit residues: 141.5857 Evaluate side-chains 145 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 435 optimal weight: 7.9990 chunk 402 optimal weight: 2.9990 chunk 431 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 376 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.095644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.055153 restraints weight = 76174.809| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.77 r_work: 0.2719 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36252 Z= 0.198 Angle : 0.519 10.672 49032 Z= 0.266 Chirality : 0.044 0.151 5478 Planarity : 0.004 0.054 6390 Dihedral : 5.384 45.648 4992 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.84 % Allowed : 8.75 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.13), residues: 4434 helix: 1.49 (0.11), residues: 2082 sheet: 0.52 (0.20), residues: 666 loop : 1.14 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.023 0.001 TYR E 173 PHE 0.009 0.001 PHE A 302 TRP 0.008 0.001 TRP D 454 HIS 0.011 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (36252) covalent geometry : angle 0.51893 / 0.27 (49032) hydrogen bonds : bond 0.03875 / 2.55 ( 1683) hydrogen bonds : angle 4.12609 / 2.92 ( 4716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6417 (mpt) cc_final: 0.6122 (mpt) REVERT: A 317 HIS cc_start: 0.8100 (m90) cc_final: 0.7718 (t-90) REVERT: B 158 MET cc_start: 0.7693 (pmm) cc_final: 0.7279 (pp-130) REVERT: B 199 ASN cc_start: 0.8903 (m110) cc_final: 0.8482 (p0) REVERT: B 225 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8755 (mmm-85) REVERT: B 508 MET cc_start: 0.9105 (ttt) cc_final: 0.8828 (tmm) REVERT: B 701 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: C 46 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6577 (mpp) REVERT: C 84 MET cc_start: 0.7710 (tpt) cc_final: 0.7033 (tmt) REVERT: C 158 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7361 (ppp) REVERT: C 199 ASN cc_start: 0.8934 (m-40) cc_final: 0.8563 (p0) REVERT: C 317 HIS cc_start: 0.8193 (m90) cc_final: 0.7837 (t-90) REVERT: D 158 MET cc_start: 0.7898 (pmm) cc_final: 0.7588 (ppp) REVERT: D 219 MET cc_start: 0.9346 (mtm) cc_final: 0.9104 (mtm) REVERT: D 225 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8732 (mmm-85) REVERT: E 158 MET cc_start: 0.7655 (pmm) cc_final: 0.7349 (ppp) REVERT: E 199 ASN cc_start: 0.8941 (m-40) cc_final: 0.8489 (p0) REVERT: E 225 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8751 (mmm-85) REVERT: E 508 MET cc_start: 0.9146 (ttt) cc_final: 0.8819 (tmm) REVERT: F 158 MET cc_start: 0.7524 (pmm) cc_final: 0.7317 (ppp) REVERT: F 199 ASN cc_start: 0.8932 (m-40) cc_final: 0.8541 (p0) outliers start: 32 outliers final: 13 residues processed: 157 average time/residue: 0.7629 time to fit residues: 144.0344 Evaluate side-chains 151 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 379 optimal weight: 0.0070 chunk 195 optimal weight: 2.9990 chunk 394 optimal weight: 2.9990 chunk 368 optimal weight: 7.9990 chunk 405 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 316 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056421 restraints weight = 75577.579| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.78 r_work: 0.2752 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36252 Z= 0.115 Angle : 0.482 10.078 49032 Z= 0.248 Chirality : 0.042 0.152 5478 Planarity : 0.004 0.051 6390 Dihedral : 4.706 37.617 4992 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.63 % Allowed : 8.89 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.13), residues: 4434 helix: 1.64 (0.12), residues: 2082 sheet: 0.51 (0.20), residues: 660 loop : 1.19 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.022 0.001 TYR E 173 PHE 0.011 0.001 PHE E 363 TRP 0.006 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (36252) covalent geometry : angle 0.48241 / 0.25 (49032) hydrogen bonds : bond 0.03273 / 2.16 ( 1683) hydrogen bonds : angle 3.98539 / 2.82 ( 4716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6284 (mpt) cc_final: 0.6009 (mpt) REVERT: A 317 HIS cc_start: 0.8112 (m90) cc_final: 0.7759 (t-90) REVERT: B 158 MET cc_start: 0.7720 (pmm) cc_final: 0.7305 (pp-130) REVERT: B 199 ASN cc_start: 0.8903 (m110) cc_final: 0.8479 (p0) REVERT: B 225 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8813 (mmm-85) REVERT: B 508 MET cc_start: 0.9102 (ttt) cc_final: 0.8774 (tmm) REVERT: B 701 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: C 46 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6618 (mtp) REVERT: C 84 MET cc_start: 0.7867 (tpt) cc_final: 0.7112 (tmt) REVERT: C 158 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7401 (ppp) REVERT: C 199 ASN cc_start: 0.8926 (m-40) cc_final: 0.8556 (p0) REVERT: C 317 HIS cc_start: 0.8218 (m90) cc_final: 0.7635 (t-90) REVERT: D 158 MET cc_start: 0.7851 (pmm) cc_final: 0.7562 (ppp) REVERT: D 219 MET cc_start: 0.9277 (mtm) cc_final: 0.9019 (mtm) REVERT: D 317 HIS cc_start: 0.8145 (m90) cc_final: 0.7720 (t70) REVERT: E 158 MET cc_start: 0.7617 (pmm) cc_final: 0.7318 (ppp) REVERT: E 199 ASN cc_start: 0.8966 (m-40) cc_final: 0.8506 (p0) REVERT: E 225 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8739 (mmm-85) REVERT: E 508 MET cc_start: 0.9138 (ttt) cc_final: 0.8804 (tmm) REVERT: F 158 MET cc_start: 0.7508 (pmm) cc_final: 0.7295 (ppp) REVERT: F 199 ASN cc_start: 0.8932 (m-40) cc_final: 0.8535 (p0) outliers start: 24 outliers final: 14 residues processed: 151 average time/residue: 0.7853 time to fit residues: 141.4086 Evaluate side-chains 152 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 239 optimal weight: 30.0000 chunk 318 optimal weight: 0.1980 chunk 169 optimal weight: 3.9990 chunk 329 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056202 restraints weight = 76218.968| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.75 r_work: 0.2748 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36252 Z= 0.132 Angle : 0.489 10.792 49032 Z= 0.251 Chirality : 0.043 0.151 5478 Planarity : 0.004 0.051 6390 Dihedral : 4.500 36.382 4992 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.68 % Allowed : 8.94 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.13), residues: 4434 helix: 1.66 (0.12), residues: 2082 sheet: 0.55 (0.20), residues: 660 loop : 1.20 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 93 TYR 0.022 0.001 TYR E 173 PHE 0.009 0.001 PHE E 363 TRP 0.008 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (36252) covalent geometry : angle 0.48930 / 0.25 (49032) hydrogen bonds : bond 0.03395 / 2.24 ( 1683) hydrogen bonds : angle 3.98575 / 2.83 ( 4716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6360 (mpt) cc_final: 0.6084 (mpt) REVERT: A 225 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8802 (mmm-85) REVERT: A 317 HIS cc_start: 0.8162 (m90) cc_final: 0.7795 (t-90) REVERT: B 199 ASN cc_start: 0.8911 (m110) cc_final: 0.8487 (p0) REVERT: B 225 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8894 (mmm-85) REVERT: B 508 MET cc_start: 0.9105 (ttt) cc_final: 0.8766 (tmm) REVERT: B 701 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: C 46 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6654 (mtp) REVERT: C 84 MET cc_start: 0.7968 (tpt) cc_final: 0.7177 (tmt) REVERT: C 199 ASN cc_start: 0.8940 (m-40) cc_final: 0.8569 (p0) REVERT: C 317 HIS cc_start: 0.8258 (m90) cc_final: 0.7654 (t-90) REVERT: D 46 MET cc_start: 0.6637 (mpt) cc_final: 0.6386 (mpt) REVERT: D 84 MET cc_start: 0.7161 (tpt) cc_final: 0.6500 (tmt) REVERT: D 158 MET cc_start: 0.7802 (pmm) cc_final: 0.7499 (ppp) REVERT: D 219 MET cc_start: 0.9290 (mtm) cc_final: 0.9063 (mtm) REVERT: D 225 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8785 (mmm-85) REVERT: D 317 HIS cc_start: 0.8157 (m90) cc_final: 0.7737 (t70) REVERT: E 158 MET cc_start: 0.7479 (pmm) cc_final: 0.6928 (pp-130) REVERT: E 199 ASN cc_start: 0.8978 (m-40) cc_final: 0.8516 (p0) REVERT: E 225 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8871 (mmm-85) REVERT: E 508 MET cc_start: 0.9148 (ttt) cc_final: 0.8793 (tmm) REVERT: F 158 MET cc_start: 0.7412 (pmm) cc_final: 0.7172 (ppp) REVERT: F 199 ASN cc_start: 0.8935 (m-40) cc_final: 0.8544 (p0) outliers start: 26 outliers final: 15 residues processed: 153 average time/residue: 0.7874 time to fit residues: 144.7101 Evaluate side-chains 154 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 260 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 318 optimal weight: 7.9990 chunk 430 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.095941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055351 restraints weight = 75473.496| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.80 r_work: 0.2722 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36252 Z= 0.186 Angle : 0.521 10.843 49032 Z= 0.266 Chirality : 0.044 0.181 5478 Planarity : 0.004 0.052 6390 Dihedral : 4.558 38.100 4992 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.66 % Allowed : 9.02 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.13), residues: 4434 helix: 1.62 (0.12), residues: 2064 sheet: 0.55 (0.20), residues: 660 loop : 1.14 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 93 TYR 0.022 0.001 TYR E 173 PHE 0.009 0.001 PHE A 302 TRP 0.008 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (36252) covalent geometry : angle 0.52076 / 0.27 (49032) hydrogen bonds : bond 0.03773 / 2.49 ( 1683) hydrogen bonds : angle 4.06138 / 2.88 ( 4716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17074.66 seconds wall clock time: 290 minutes 3.49 seconds (17403.49 seconds total)