Starting phenix.real_space_refine on Fri Mar 6 21:48:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln1_23445/03_2026/7ln1_23445.map" } resolution = 3.4 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= 0.002 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 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21790 2.51 5 N 6171 2.21 5 O 6619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34796 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5698 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5778 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 661} Chain breaks: 5 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: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.47, per 1000 atoms: 0.24 Number of scatterers: 34796 At special positions: 0 Unit cell: (162.639, 171.143, 136.064, 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 178 16.00 P 31 15.00 Mg 7 11.99 O 6619 8.00 N 6171 7.00 C 21790 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: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 29 sheets defined 51.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.065A pdb=" N GLU A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.084A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.702A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.509A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 402 removed outlier: 4.460A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.568A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.938A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.860A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.333A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.748A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 612 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 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.684A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.812A pdb=" N GLU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.315A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.082A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.850A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.619A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.828A pdb=" N GLY B 334 " --> pdb=" O THR B 330 " (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 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 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 removed outlier: 3.746A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.885A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.581A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.309A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.553A pdb=" N LEU B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.646A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.689A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.594A pdb=" N ARG C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.560A pdb=" N GLU C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.540A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.106A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.617A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.817A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.155A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 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: 3.742A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 578 through 583 removed outlier: 4.437A pdb=" N ILE C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.700A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (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 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.656A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.995A pdb=" N GLY C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.666A pdb=" N LYS D 18 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.641A pdb=" N GLU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.655A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.196A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.019A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.538A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.647A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 461 through 465 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: 3.920A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 543 through 547 removed outlier: 3.690A pdb=" N GLU D 546 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 543 through 547' Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.580A pdb=" N ALA D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.046A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 4.024A pdb=" N GLY D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.638A pdb=" N LEU D 634 " --> pdb=" O ASP D 630 " (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 Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.597A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 removed outlier: 4.025A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.851A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 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 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: 3.545A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.740A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 272 through 275 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.206A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.897A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (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 removed outlier: 3.806A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.557A pdb=" N ARG E 465 " --> pdb=" O SER E 462 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU E 466 " --> pdb=" O ALA E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.932A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 553 through 569 Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.930A pdb=" N ARG E 599 " --> pdb=" O GLY E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.824A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (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 Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 748 through 766 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.686A 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 Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.125A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.506A 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 277 removed outlier: 3.758A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.631A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.002A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.503A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.572A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.964A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.522A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.806A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.668A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.601A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.674A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.696A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.838A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 3.870A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.387A pdb=" N ALA A 177 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG A 113 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N ASP A 179 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N HIS A 115 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N VAL A 181 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N LEU A 117 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N HIS A 183 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.443A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.802A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.406A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 40 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 154 removed outlier: 4.265A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.702A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.091A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.378A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.968A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.553A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.652A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.384A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 29 removed outlier: 6.258A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.058A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.488A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.536A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.370A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.771A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.222A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.447A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.998A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 40 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 71 " --> pdb=" O ASP F 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 60 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 151 through 154 removed outlier: 5.329A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS F 115 " --> pdb=" O GLU F 167 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.504A pdb=" N ILE F 146 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 266 through 270 removed outlier: 6.836A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.180A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 514 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1597 hydrogen bonds defined for protein. 4638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.15 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11871 1.34 - 1.46: 6679 1.46 - 1.58: 16519 1.58 - 1.70: 25 1.70 - 1.83: 284 Bond restraints: 35378 Sorted by residual: bond pdb=" CG PRO F 44 " pdb=" CD PRO F 44 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.63e+00 bond pdb=" C VAL D 235 " pdb=" N LYS D 236 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.47e-02 4.63e+03 3.85e+00 bond pdb=" CG1 ILE D 601 " pdb=" CD1 ILE D 601 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.37e+00 bond pdb=" O3A ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.592 1.540 0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" O3B ATP E 902 " pdb=" PB ATP E 902 " ideal model delta sigma weight residual 1.592 1.542 0.050 3.00e-02 1.11e+03 2.79e+00 ... (remaining 35373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 46600 2.04 - 4.07: 1061 4.07 - 6.11: 149 6.11 - 8.14: 16 8.14 - 10.18: 6 Bond angle restraints: 47832 Sorted by residual: angle pdb=" N PRO F 44 " pdb=" CD PRO F 44 " pdb=" CG PRO F 44 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO F 44 " pdb=" N PRO F 44 " pdb=" CD PRO F 44 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" C VAL D 235 " pdb=" N LYS D 236 " pdb=" CA LYS D 236 " ideal model delta sigma weight residual 120.68 127.86 -7.18 1.52e+00 4.33e-01 2.23e+01 angle pdb=" C ILE E 309 " pdb=" CA ILE E 309 " pdb=" CB ILE E 309 " ideal model delta sigma weight residual 110.95 105.66 5.29 1.48e+00 4.57e-01 1.28e+01 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 106.21 109.89 -3.68 1.07e+00 8.73e-01 1.18e+01 ... (remaining 47827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 21418 32.83 - 65.65: 570 65.65 - 98.48: 63 98.48 - 131.31: 3 131.31 - 164.14: 6 Dihedral angle restraints: 22060 sinusoidal: 9358 harmonic: 12702 Sorted by residual: dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 104.13 -164.14 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 81.11 -141.11 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 22057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3982 0.048 - 0.097: 1096 0.097 - 0.145: 283 0.145 - 0.193: 10 0.193 - 0.242: 2 Chirality restraints: 5373 Sorted by residual: chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE F 619 " pdb=" CA ILE F 619 " pdb=" CG1 ILE F 619 " pdb=" CG2 ILE F 619 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CA ILE C 269 " pdb=" N ILE C 269 " pdb=" C ILE C 269 " pdb=" CB ILE C 269 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 5370 not shown) Planarity restraints: 6263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 773 " 0.059 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO D 774 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 774 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 774 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 454 " -0.015 2.00e-02 2.50e+03 1.84e-02 8.47e+00 pdb=" CG TRP B 454 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 454 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 454 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 454 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 454 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO C 545 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.036 5.00e-02 4.00e+02 ... (remaining 6260 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 208 2.51 - 3.11: 26224 3.11 - 3.70: 55243 3.70 - 4.30: 79210 4.30 - 4.90: 129418 Nonbonded interactions: 290303 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 1.912 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 904 " model vdw 1.915 2.170 nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.922 2.170 nonbonded pdb=" O3G ATP D 901 " pdb="MG MG D 904 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 904 " model vdw 1.969 2.170 ... (remaining 290298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'B' and (resid 23 through 507 or (resid 508 and (name N or name CA or nam \ e C or name O or name CB )) or resid 509 through 545 or resid 558 through 583 or \ resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 762)) } 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: 2.180 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.670 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 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 : 0.006 0.073 35378 Z= 0.258 Angle : 0.756 10.176 47832 Z= 0.406 Chirality : 0.047 0.242 5373 Planarity : 0.006 0.088 6263 Dihedral : 14.961 164.136 13816 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 0.59 (0.12), residues: 4366 helix: 0.71 (0.11), residues: 1960 sheet: 0.58 (0.21), residues: 609 loop : 0.15 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 424 TYR 0.022 0.002 TYR F 517 PHE 0.025 0.002 PHE A 302 TRP 0.049 0.003 TRP B 454 HIS 0.012 0.002 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00613 (35378) covalent geometry : angle 0.75564 (47832) hydrogen bonds : bond 0.16752 ( 1597) hydrogen bonds : angle 6.57802 ( 4638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 508 MET cc_start: 0.7773 (mmm) cc_final: 0.7564 (mmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2396 time to fit residues: 79.0389 Evaluate side-chains 143 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 602 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.080336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054459 restraints weight = 164492.801| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.12 r_work: 0.2907 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35378 Z= 0.159 Angle : 0.610 8.915 47832 Z= 0.309 Chirality : 0.043 0.175 5373 Planarity : 0.005 0.068 6263 Dihedral : 11.073 165.685 5085 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 0.22 % Allowed : 5.55 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.02 (0.13), residues: 4366 helix: 1.22 (0.12), residues: 1963 sheet: 0.34 (0.20), residues: 633 loop : 0.37 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 365 TYR 0.018 0.002 TYR A 134 PHE 0.015 0.001 PHE E 302 TRP 0.024 0.002 TRP B 454 HIS 0.010 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00354 (35378) covalent geometry : angle 0.60999 (47832) hydrogen bonds : bond 0.04599 ( 1597) hydrogen bonds : angle 5.04707 ( 4638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 MET cc_start: 0.3386 (OUTLIER) cc_final: 0.2335 (mtp) REVERT: C 443 ASN cc_start: 0.9092 (m110) cc_final: 0.8885 (p0) REVERT: D 46 MET cc_start: 0.7560 (mtm) cc_final: 0.7161 (mtt) REVERT: D 51 LEU cc_start: 0.8059 (mt) cc_final: 0.7755 (mt) REVERT: D 84 MET cc_start: 0.8552 (ptm) cc_final: 0.8221 (tmm) REVERT: D 332 MET cc_start: 0.8785 (mtp) cc_final: 0.8502 (mtp) REVERT: D 449 MET cc_start: 0.9147 (tpt) cc_final: 0.8936 (tpp) REVERT: D 508 MET cc_start: 0.9260 (mmm) cc_final: 0.8977 (mmm) REVERT: F 489 LEU cc_start: 0.9030 (tp) cc_final: 0.8538 (mt) REVERT: F 508 MET cc_start: 0.4448 (mmm) cc_final: 0.3949 (mmm) REVERT: F 740 MET cc_start: 0.8721 (mmm) cc_final: 0.8485 (mmm) outliers start: 8 outliers final: 1 residues processed: 159 average time/residue: 0.2151 time to fit residues: 57.3522 Evaluate side-chains 140 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain F residue 179 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 387 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 82 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 251 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 533 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 602 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 260 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.078143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051083 restraints weight = 164541.047| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.51 r_work: 0.2896 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 35378 Z= 0.282 Angle : 0.665 7.226 47832 Z= 0.333 Chirality : 0.045 0.169 5373 Planarity : 0.005 0.068 6263 Dihedral : 10.911 179.492 5085 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.49 % Allowed : 7.93 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.01 (0.13), residues: 4366 helix: 1.26 (0.12), residues: 1972 sheet: 0.17 (0.20), residues: 639 loop : 0.36 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 89 TYR 0.017 0.002 TYR A 134 PHE 0.018 0.002 PHE A 302 TRP 0.018 0.002 TRP B 454 HIS 0.011 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00640 (35378) covalent geometry : angle 0.66492 (47832) hydrogen bonds : bond 0.04421 ( 1597) hydrogen bonds : angle 4.94258 ( 4638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.9275 (tpp) cc_final: 0.9014 (tpp) REVERT: C 46 MET cc_start: 0.3418 (OUTLIER) cc_final: 0.2349 (mtp) REVERT: D 46 MET cc_start: 0.7387 (mtm) cc_final: 0.6898 (mtt) REVERT: D 51 LEU cc_start: 0.8208 (mt) cc_final: 0.7875 (mt) REVERT: D 332 MET cc_start: 0.9183 (mtp) cc_final: 0.8976 (mtp) REVERT: D 508 MET cc_start: 0.9284 (mmm) cc_final: 0.8900 (mmm) REVERT: E 611 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8944 (tpp) REVERT: E 678 MET cc_start: 0.9300 (mmp) cc_final: 0.9100 (mmp) REVERT: F 449 MET cc_start: 0.8741 (mmm) cc_final: 0.8373 (mmm) REVERT: F 489 LEU cc_start: 0.9034 (tp) cc_final: 0.8581 (mt) REVERT: F 508 MET cc_start: 0.4489 (mmm) cc_final: 0.4112 (mmm) REVERT: F 740 MET cc_start: 0.8736 (mmm) cc_final: 0.8521 (mmm) outliers start: 18 outliers final: 7 residues processed: 151 average time/residue: 0.2031 time to fit residues: 52.6905 Evaluate side-chains 141 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 179 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 296 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 414 optimal weight: 30.0000 chunk 380 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 50.0000 chunk 292 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.078560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052712 restraints weight = 162270.699| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.63 r_work: 0.2888 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35378 Z= 0.179 Angle : 0.576 7.359 47832 Z= 0.287 Chirality : 0.043 0.160 5373 Planarity : 0.004 0.066 6263 Dihedral : 10.583 170.525 5085 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Rotamer: Outliers : 0.81 % Allowed : 9.63 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.13), residues: 4366 helix: 1.48 (0.12), residues: 1963 sheet: 0.12 (0.20), residues: 637 loop : 0.45 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 83 TYR 0.017 0.001 TYR A 134 PHE 0.027 0.001 PHE B 674 TRP 0.010 0.001 TRP B 454 HIS 0.008 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00406 (35378) covalent geometry : angle 0.57620 (47832) hydrogen bonds : bond 0.03833 ( 1597) hydrogen bonds : angle 4.69344 ( 4638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.6756 (tmm) cc_final: 0.6493 (tmm) REVERT: B 219 MET cc_start: 0.9353 (tpp) cc_final: 0.9103 (tpp) REVERT: C 84 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.6217 (ttm) REVERT: C 163 PHE cc_start: 0.7697 (m-10) cc_final: 0.7315 (m-80) REVERT: D 46 MET cc_start: 0.7625 (mtm) cc_final: 0.6944 (mtm) REVERT: D 84 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8287 (tmm) REVERT: D 332 MET cc_start: 0.9166 (mtp) cc_final: 0.8954 (mtp) REVERT: D 508 MET cc_start: 0.9321 (mmm) cc_final: 0.8937 (mmm) REVERT: F 489 LEU cc_start: 0.8973 (tp) cc_final: 0.8523 (mt) REVERT: F 508 MET cc_start: 0.4623 (mmm) cc_final: 0.3978 (mmm) REVERT: F 611 MET cc_start: 0.3955 (mmt) cc_final: 0.3666 (mmm) REVERT: F 740 MET cc_start: 0.8747 (mmm) cc_final: 0.8527 (mmm) outliers start: 30 outliers final: 13 residues processed: 156 average time/residue: 0.2038 time to fit residues: 55.2144 Evaluate side-chains 146 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 35 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 342 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 chunk 203 optimal weight: 0.3980 chunk 343 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 660 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.078757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053478 restraints weight = 163295.202| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.80 r_work: 0.2892 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35378 Z= 0.152 Angle : 0.563 9.364 47832 Z= 0.277 Chirality : 0.042 0.196 5373 Planarity : 0.004 0.066 6263 Dihedral : 10.345 162.660 5085 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 0.89 % Allowed : 10.60 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.31 (0.13), residues: 4366 helix: 1.60 (0.12), residues: 1974 sheet: 0.06 (0.20), residues: 643 loop : 0.50 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 753 TYR 0.022 0.001 TYR B 138 PHE 0.013 0.001 PHE B 576 TRP 0.007 0.001 TRP B 551 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00344 (35378) covalent geometry : angle 0.56277 (47832) hydrogen bonds : bond 0.03582 ( 1597) hydrogen bonds : angle 4.53168 ( 4638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9164 (ttp) cc_final: 0.8645 (tmm) REVERT: B 219 MET cc_start: 0.9333 (tpp) cc_final: 0.9057 (tpp) REVERT: C 163 PHE cc_start: 0.7688 (m-10) cc_final: 0.7321 (m-80) REVERT: C 281 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: D 46 MET cc_start: 0.7773 (mtm) cc_final: 0.7144 (mtt) REVERT: D 84 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8347 (tmm) REVERT: D 332 MET cc_start: 0.9203 (mtp) cc_final: 0.8983 (mtp) REVERT: D 508 MET cc_start: 0.9334 (mmm) cc_final: 0.8975 (mmm) REVERT: E 504 LEU cc_start: 0.9443 (tp) cc_final: 0.9158 (pp) REVERT: E 611 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8907 (tpp) REVERT: F 449 MET cc_start: 0.8760 (mmm) cc_final: 0.8462 (mmm) REVERT: F 508 MET cc_start: 0.4612 (mmm) cc_final: 0.3983 (mmm) REVERT: F 611 MET cc_start: 0.4045 (mmt) cc_final: 0.3770 (mmm) REVERT: F 740 MET cc_start: 0.8745 (mmm) cc_final: 0.8527 (mmm) outliers start: 33 outliers final: 15 residues processed: 162 average time/residue: 0.1981 time to fit residues: 55.0317 Evaluate side-chains 146 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 345 optimal weight: 0.8980 chunk 141 optimal weight: 0.0980 chunk 231 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.078419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052440 restraints weight = 163023.047| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.77 r_work: 0.2882 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35378 Z= 0.161 Angle : 0.566 12.705 47832 Z= 0.277 Chirality : 0.042 0.161 5373 Planarity : 0.004 0.063 6263 Dihedral : 10.202 154.958 5085 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.11 % Allowed : 11.40 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.36 (0.13), residues: 4366 helix: 1.68 (0.12), residues: 1962 sheet: 0.06 (0.20), residues: 650 loop : 0.50 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.012 0.001 TYR B 138 PHE 0.011 0.001 PHE A 302 TRP 0.007 0.001 TRP B 551 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00367 (35378) covalent geometry : angle 0.56603 (47832) hydrogen bonds : bond 0.03517 ( 1597) hydrogen bonds : angle 4.48845 ( 4638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9328 (ttp) cc_final: 0.8862 (tmm) REVERT: B 219 MET cc_start: 0.9342 (tpp) cc_final: 0.9074 (tpp) REVERT: C 163 PHE cc_start: 0.7750 (m-10) cc_final: 0.7332 (m-80) REVERT: C 281 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: D 46 MET cc_start: 0.7893 (mtm) cc_final: 0.7238 (mtt) REVERT: D 84 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8340 (tmm) REVERT: D 139 PHE cc_start: 0.8022 (m-80) cc_final: 0.7159 (m-10) REVERT: D 332 MET cc_start: 0.9232 (mtp) cc_final: 0.9019 (mtp) REVERT: D 508 MET cc_start: 0.9343 (mmm) cc_final: 0.8955 (mmm) REVERT: E 475 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9229 (p) REVERT: E 504 LEU cc_start: 0.9449 (tp) cc_final: 0.9162 (pp) REVERT: E 611 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8833 (tpp) REVERT: F 449 MET cc_start: 0.8775 (mmm) cc_final: 0.8439 (mmm) REVERT: F 508 MET cc_start: 0.4630 (mmm) cc_final: 0.3980 (mmm) REVERT: F 611 MET cc_start: 0.4122 (mmt) cc_final: 0.3886 (mmm) REVERT: F 740 MET cc_start: 0.8769 (mmm) cc_final: 0.8553 (mmm) outliers start: 41 outliers final: 24 residues processed: 161 average time/residue: 0.1956 time to fit residues: 54.0945 Evaluate side-chains 155 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 279 optimal weight: 0.5980 chunk 280 optimal weight: 0.5980 chunk 333 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 158 optimal weight: 0.0060 chunk 313 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 220 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 602 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053905 restraints weight = 162728.041| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.79 r_work: 0.2928 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35378 Z= 0.098 Angle : 0.546 21.019 47832 Z= 0.264 Chirality : 0.042 0.189 5373 Planarity : 0.004 0.063 6263 Dihedral : 9.837 152.028 5085 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 0.92 % Allowed : 11.92 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.45 (0.13), residues: 4366 helix: 1.79 (0.12), residues: 1969 sheet: 0.10 (0.20), residues: 649 loop : 0.50 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 377 TYR 0.013 0.001 TYR B 138 PHE 0.021 0.001 PHE B 152 TRP 0.006 0.001 TRP B 551 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00217 (35378) covalent geometry : angle 0.54629 (47832) hydrogen bonds : bond 0.03256 ( 1597) hydrogen bonds : angle 4.33014 ( 4638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.9325 (tpp) cc_final: 0.9059 (tpp) REVERT: C 163 PHE cc_start: 0.7731 (m-10) cc_final: 0.7218 (m-80) REVERT: C 281 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: D 46 MET cc_start: 0.7942 (mtm) cc_final: 0.7288 (mtt) REVERT: D 84 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8248 (tmm) REVERT: D 139 PHE cc_start: 0.7954 (m-80) cc_final: 0.7130 (m-10) REVERT: D 508 MET cc_start: 0.9339 (mmm) cc_final: 0.8986 (mmm) REVERT: E 475 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9199 (p) REVERT: E 504 LEU cc_start: 0.9454 (tp) cc_final: 0.9170 (pp) REVERT: E 611 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8841 (tpp) REVERT: E 669 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.7954 (p0) REVERT: F 449 MET cc_start: 0.8767 (mmm) cc_final: 0.8434 (mmm) REVERT: F 508 MET cc_start: 0.4665 (mmm) cc_final: 0.4001 (mmm) REVERT: F 740 MET cc_start: 0.8741 (mmm) cc_final: 0.8519 (mmm) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 0.2025 time to fit residues: 56.1062 Evaluate side-chains 149 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 270 optimal weight: 0.0980 chunk 10 optimal weight: 0.0370 chunk 394 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 354 optimal weight: 0.9980 chunk 78 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 290 optimal weight: 7.9990 chunk 380 optimal weight: 0.8980 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.079748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054526 restraints weight = 163279.172| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.81 r_work: 0.2946 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35378 Z= 0.096 Angle : 0.542 10.013 47832 Z= 0.261 Chirality : 0.042 0.201 5373 Planarity : 0.004 0.063 6263 Dihedral : 9.452 145.186 5085 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 0.81 % Allowed : 12.13 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.50 (0.13), residues: 4366 helix: 1.83 (0.12), residues: 1978 sheet: 0.18 (0.20), residues: 645 loop : 0.51 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 362 TYR 0.009 0.001 TYR F 203 PHE 0.032 0.001 PHE B 674 TRP 0.005 0.001 TRP E 551 HIS 0.004 0.000 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00210 (35378) covalent geometry : angle 0.54206 (47832) hydrogen bonds : bond 0.03093 ( 1597) hydrogen bonds : angle 4.25944 ( 4638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.8362 (mtm) cc_final: 0.7925 (pmm) REVERT: B 219 MET cc_start: 0.9321 (tpp) cc_final: 0.9095 (tpp) REVERT: C 163 PHE cc_start: 0.7771 (m-10) cc_final: 0.7272 (m-80) REVERT: C 281 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 46 MET cc_start: 0.7990 (mtm) cc_final: 0.7345 (mtt) REVERT: D 84 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: D 139 PHE cc_start: 0.8010 (m-80) cc_final: 0.7218 (m-10) REVERT: D 508 MET cc_start: 0.9349 (mmm) cc_final: 0.9023 (mmm) REVERT: E 475 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9193 (p) REVERT: E 504 LEU cc_start: 0.9437 (tp) cc_final: 0.9150 (pp) REVERT: E 611 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8839 (tpp) REVERT: E 669 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.7955 (p0) REVERT: E 757 MET cc_start: 0.9096 (tmm) cc_final: 0.8789 (tmm) REVERT: F 508 MET cc_start: 0.4655 (mmm) cc_final: 0.4042 (mmm) REVERT: F 611 MET cc_start: 0.5169 (mmm) cc_final: 0.4875 (ppp) REVERT: F 740 MET cc_start: 0.8742 (mmm) cc_final: 0.8516 (mmm) outliers start: 30 outliers final: 16 residues processed: 154 average time/residue: 0.1940 time to fit residues: 52.5392 Evaluate side-chains 148 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 410 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 330 optimal weight: 0.0070 chunk 284 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 365 optimal weight: 0.0270 overall best weight: 2.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 260 ASN F 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.078747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052627 restraints weight = 163863.913| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.87 r_work: 0.2907 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35378 Z= 0.142 Angle : 0.552 9.628 47832 Z= 0.267 Chirality : 0.042 0.171 5373 Planarity : 0.004 0.059 6263 Dihedral : 9.453 136.703 5085 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 0.70 % Allowed : 12.40 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.57 (0.13), residues: 4366 helix: 1.87 (0.12), residues: 1981 sheet: 0.17 (0.20), residues: 660 loop : 0.56 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.014 0.001 TYR B 138 PHE 0.023 0.001 PHE B 674 TRP 0.010 0.001 TRP A 551 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00324 (35378) covalent geometry : angle 0.55245 (47832) hydrogen bonds : bond 0.03227 ( 1597) hydrogen bonds : angle 4.28277 ( 4638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.9344 (tpp) cc_final: 0.9135 (tpp) REVERT: C 163 PHE cc_start: 0.7743 (m-10) cc_final: 0.7382 (m-80) REVERT: C 281 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8287 (mt-10) REVERT: D 46 MET cc_start: 0.7887 (mtm) cc_final: 0.7140 (mtt) REVERT: D 84 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8186 (tmm) REVERT: D 139 PHE cc_start: 0.8111 (m-80) cc_final: 0.7334 (m-10) REVERT: D 508 MET cc_start: 0.9375 (mmm) cc_final: 0.9012 (mmm) REVERT: E 475 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9213 (p) REVERT: E 504 LEU cc_start: 0.9452 (tp) cc_final: 0.9163 (pp) REVERT: E 611 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8789 (tpp) REVERT: E 669 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.7985 (p0) REVERT: F 427 MET cc_start: 0.9194 (tpt) cc_final: 0.8911 (tpt) REVERT: F 508 MET cc_start: 0.4418 (mmm) cc_final: 0.3712 (mmm) REVERT: F 611 MET cc_start: 0.5099 (mmm) cc_final: 0.4724 (ppp) REVERT: F 740 MET cc_start: 0.8789 (mmm) cc_final: 0.8573 (mmm) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 0.1949 time to fit residues: 50.5090 Evaluate side-chains 150 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 296 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 393 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 231 optimal weight: 20.0000 chunk 422 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052495 restraints weight = 164716.593| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.78 r_work: 0.2896 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35378 Z= 0.149 Angle : 0.564 10.217 47832 Z= 0.273 Chirality : 0.042 0.173 5373 Planarity : 0.004 0.057 6263 Dihedral : 9.385 127.724 5085 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 0.73 % Allowed : 12.40 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.55 (0.13), residues: 4366 helix: 1.85 (0.12), residues: 1974 sheet: 0.16 (0.20), residues: 650 loop : 0.56 (0.16), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 53 TYR 0.010 0.001 TYR B 138 PHE 0.025 0.001 PHE B 674 TRP 0.007 0.001 TRP A 551 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00340 (35378) covalent geometry : angle 0.56400 (47832) hydrogen bonds : bond 0.03276 ( 1597) hydrogen bonds : angle 4.31333 ( 4638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.9331 (tpp) cc_final: 0.9119 (tpp) REVERT: B 508 MET cc_start: 0.7926 (ptm) cc_final: 0.7698 (ptm) REVERT: C 163 PHE cc_start: 0.7781 (m-10) cc_final: 0.7341 (m-80) REVERT: C 281 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: C 449 MET cc_start: 0.7407 (mmm) cc_final: 0.7052 (mmm) REVERT: D 46 MET cc_start: 0.7878 (mtm) cc_final: 0.7349 (mtm) REVERT: D 84 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8270 (tmm) REVERT: D 139 PHE cc_start: 0.8046 (m-80) cc_final: 0.7468 (m-10) REVERT: D 508 MET cc_start: 0.9357 (mmm) cc_final: 0.8956 (mmm) REVERT: E 475 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9224 (p) REVERT: E 504 LEU cc_start: 0.9459 (tp) cc_final: 0.9172 (pp) REVERT: E 611 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8800 (tpp) REVERT: E 669 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.7984 (p0) REVERT: F 427 MET cc_start: 0.9164 (tpt) cc_final: 0.8892 (tpt) REVERT: F 508 MET cc_start: 0.4730 (mmm) cc_final: 0.4010 (mmm) REVERT: F 611 MET cc_start: 0.5161 (mmm) cc_final: 0.4874 (ppp) REVERT: F 740 MET cc_start: 0.8794 (mmm) cc_final: 0.8580 (mmm) outliers start: 27 outliers final: 20 residues processed: 147 average time/residue: 0.1995 time to fit residues: 51.5280 Evaluate side-chains 151 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 257 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 325 optimal weight: 0.0270 chunk 355 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.078772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052095 restraints weight = 162730.618| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.51 r_work: 0.2941 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35378 Z= 0.117 Angle : 0.548 9.785 47832 Z= 0.265 Chirality : 0.042 0.178 5373 Planarity : 0.004 0.058 6263 Dihedral : 9.135 128.360 5085 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 0.84 % Allowed : 12.27 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.13), residues: 4366 helix: 1.88 (0.12), residues: 1986 sheet: 0.18 (0.20), residues: 650 loop : 0.56 (0.16), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.009 0.001 TYR B 138 PHE 0.023 0.001 PHE B 674 TRP 0.006 0.001 TRP A 551 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00267 (35378) covalent geometry : angle 0.54805 (47832) hydrogen bonds : bond 0.03134 ( 1597) hydrogen bonds : angle 4.24560 ( 4638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9510.86 seconds wall clock time: 163 minutes 15.43 seconds (9795.43 seconds total)