Starting phenix.real_space_refine on Fri Mar 6 21:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jy5_22521/03_2026/7jy5_22521.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21732 2.51 5 N 6156 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 312 residue(s): 0.03s 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: 34728 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 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, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.39, per 1000 atoms: 0.21 Number of scatterers: 34728 At special positions: 0 Unit cell: (175.56, 170.28, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6600 8.00 N 6156 7.00 C 21732 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 30 sheets defined 52.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 43 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 92 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.545A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.845A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.017A 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 233 removed outlier: 3.915A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.513A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.766A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.107A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.696A 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 543 through 549 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 611 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.776A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 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 742 removed outlier: 3.839A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 762 through 766 removed outlier: 4.268A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.544A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.845A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.017A 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 233 removed outlier: 3.914A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.512A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.000A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.766A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.107A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) 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 425 Processing helix chain 'B' and resid 426 through 430 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 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.696A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 611 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.776A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.839A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 759 Processing helix chain 'B' and resid 762 through 766 removed outlier: 4.268A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 43 through 50 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 92 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.545A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.845A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.016A 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 233 removed outlier: 3.915A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.512A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.765A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 4.107A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.695A 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 543 through 549 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 611 Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.776A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 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: 3.839A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 759 Processing helix chain 'C' and resid 762 through 766 removed outlier: 4.267A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.545A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.845A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.017A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.915A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.512A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.766A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 4.106A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.695A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 549 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 611 Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.776A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 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 742 removed outlier: 3.839A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 759 Processing helix chain 'D' and resid 762 through 766 removed outlier: 4.267A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.545A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.844A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.016A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.915A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.512A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.766A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.107A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.695A 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 543 through 549 Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 611 Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.775A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 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 742 removed outlier: 3.839A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 759 Processing helix chain 'E' and resid 762 through 766 removed outlier: 4.268A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 18 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.545A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.510A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.845A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.016A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.915A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.512A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.765A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 4.107A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.696A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 549 Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 578 through 585 removed outlier: 3.989A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 611 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.776A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.838A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 759 Processing helix chain 'F' and resid 762 through 766 removed outlier: 4.268A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 6.989A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS A 81 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER A 42 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.662A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.374A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.600A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 30 removed outlier: 6.989A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.663A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.376A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.601A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 30 removed outlier: 6.989A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.662A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.374A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 541 removed outlier: 6.601A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 6.989A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.662A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.375A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 541 removed outlier: 6.600A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 30 removed outlier: 6.988A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.662A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.375A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 541 removed outlier: 6.600A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 30 removed outlier: 6.989A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS F 81 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER F 42 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 154 removed outlier: 6.662A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.375A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 541 removed outlier: 6.600A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1620 hydrogen bonds defined for protein. 4572 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: 8.39 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12217 1.36 - 1.51: 10109 1.51 - 1.65: 12648 1.65 - 1.79: 184 1.79 - 1.94: 116 Bond restraints: 35274 Sorted by residual: bond pdb=" CB ARG E 377 " pdb=" CG ARG E 377 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.17e+00 bond pdb=" CG1 ILE F 645 " pdb=" CD1 ILE F 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.16e+00 bond pdb=" CB ARG F 377 " pdb=" CG ARG F 377 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CG1 ILE B 645 " pdb=" CD1 ILE B 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.14e+00 bond pdb=" CG1 ILE A 645 " pdb=" CD1 ILE A 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.13e+00 ... (remaining 35269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 45282 1.37 - 2.74: 1997 2.74 - 4.12: 355 4.12 - 5.49: 30 5.49 - 6.86: 36 Bond angle restraints: 47700 Sorted by residual: angle pdb=" NE ARG E 465 " pdb=" CZ ARG E 465 " pdb=" NH1 ARG E 465 " ideal model delta sigma weight residual 121.50 119.20 2.30 1.00e+00 1.00e+00 5.31e+00 angle pdb=" NE ARG B 465 " pdb=" CZ ARG B 465 " pdb=" NH1 ARG B 465 " ideal model delta sigma weight residual 121.50 119.21 2.29 1.00e+00 1.00e+00 5.24e+00 angle pdb=" NE ARG A 465 " pdb=" CZ ARG A 465 " pdb=" NH1 ARG A 465 " ideal model delta sigma weight residual 121.50 119.24 2.26 1.00e+00 1.00e+00 5.12e+00 angle pdb=" NE ARG F 465 " pdb=" CZ ARG F 465 " pdb=" NH1 ARG F 465 " ideal model delta sigma weight residual 121.50 119.24 2.26 1.00e+00 1.00e+00 5.10e+00 angle pdb=" NE ARG C 465 " pdb=" CZ ARG C 465 " pdb=" NH1 ARG C 465 " ideal model delta sigma weight residual 121.50 119.25 2.25 1.00e+00 1.00e+00 5.05e+00 ... (remaining 47695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.71: 21409 30.71 - 61.41: 551 61.41 - 92.12: 54 92.12 - 122.82: 6 122.82 - 153.53: 6 Dihedral angle restraints: 22026 sinusoidal: 9342 harmonic: 12684 Sorted by residual: dihedral pdb=" O1A AGS C 903 " pdb=" O3A AGS C 903 " pdb=" PA AGS C 903 " pdb=" PB AGS C 903 " ideal model delta sinusoidal sigma weight residual -67.73 85.80 -153.53 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O1A AGS F 903 " pdb=" O3A AGS F 903 " pdb=" PA AGS F 903 " pdb=" PB AGS F 903 " ideal model delta sinusoidal sigma weight residual -67.73 85.46 -153.19 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA ASN F 296 " pdb=" C ASN F 296 " pdb=" N ALA F 297 " pdb=" CA ALA F 297 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 22023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3490 0.046 - 0.093: 1489 0.093 - 0.139: 434 0.139 - 0.185: 17 0.185 - 0.232: 6 Chirality restraints: 5436 Sorted by residual: chirality pdb=" PA AGS A 904 " pdb=" O2A AGS A 904 " pdb=" O3A AGS A 904 " pdb=" O5' AGS A 904 " both_signs ideal model delta sigma weight residual True 3.18 2.95 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" PA AGS D 904 " pdb=" O2A AGS D 904 " pdb=" O3A AGS D 904 " pdb=" O5' AGS D 904 " both_signs ideal model delta sigma weight residual True 3.18 2.95 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" PA AGS E 904 " pdb=" O2A AGS E 904 " pdb=" O3A AGS E 904 " pdb=" O5' AGS E 904 " both_signs ideal model delta sigma weight residual True 3.18 2.96 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 5433 not shown) Planarity restraints: 6222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO E 545 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 545 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 544 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO F 545 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 545 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 545 " 0.028 5.00e-02 4.00e+02 ... (remaining 6219 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 155 2.49 - 3.09: 24350 3.09 - 3.69: 53215 3.69 - 4.30: 80763 4.30 - 4.90: 133328 Nonbonded interactions: 291811 Sorted by model distance: nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 901 " model vdw 1.883 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 901 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 901 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 901 " model vdw 1.890 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 901 " model vdw 1.897 2.170 ... (remaining 291806 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.970 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.009 0.069 35274 Z= 0.358 Angle : 0.672 6.859 47700 Z= 0.366 Chirality : 0.052 0.232 5436 Planarity : 0.004 0.050 6222 Dihedral : 14.156 153.525 13770 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.30 (0.13), residues: 4338 helix: -0.55 (0.11), residues: 2046 sheet: 0.53 (0.22), residues: 576 loop : 0.30 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 741 TYR 0.016 0.002 TYR A 203 PHE 0.010 0.002 PHE D 758 TRP 0.012 0.003 TRP E 454 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00861 (35274) covalent geometry : angle 0.67162 (47700) hydrogen bonds : bond 0.18946 ( 1620) hydrogen bonds : angle 6.73216 ( 4572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.271 Fit side-chains REVERT: B 449 MET cc_start: 0.7990 (tpt) cc_final: 0.7762 (tpt) REVERT: E 449 MET cc_start: 0.7936 (tpt) cc_final: 0.7678 (tpt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.8179 time to fit residues: 199.8879 Evaluate side-chains 140 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.092996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056540 restraints weight = 83229.999| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.20 r_work: 0.2692 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35274 Z= 0.132 Angle : 0.576 9.227 47700 Z= 0.292 Chirality : 0.046 0.229 5436 Planarity : 0.005 0.049 6222 Dihedral : 9.796 151.514 5004 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.99 % Allowed : 4.51 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.46 (0.13), residues: 4338 helix: 0.33 (0.11), residues: 2070 sheet: -0.08 (0.21), residues: 678 loop : 0.78 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 662 TYR 0.007 0.001 TYR A 203 PHE 0.008 0.001 PHE E 290 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00300 (35274) covalent geometry : angle 0.57583 (47700) hydrogen bonds : bond 0.04006 ( 1620) hydrogen bonds : angle 4.87903 ( 4572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.111 Fit side-chains REVERT: A 84 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7630 (pp-130) REVERT: A 158 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5800 (pp-130) REVERT: B 158 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6401 (pp-130) REVERT: B 201 VAL cc_start: 0.8970 (t) cc_final: 0.8663 (t) REVERT: B 427 MET cc_start: 0.8584 (mtp) cc_final: 0.8287 (mmm) REVERT: B 449 MET cc_start: 0.8758 (tpt) cc_final: 0.8445 (tpt) REVERT: C 84 MET cc_start: 0.8914 (ptp) cc_final: 0.8563 (ttp) REVERT: C 158 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5804 (pp-130) REVERT: C 273 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8867 (tm-30) REVERT: D 84 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7589 (pp-130) REVERT: D 158 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5840 (pp-130) REVERT: D 273 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8454 (tp30) REVERT: D 611 MET cc_start: 0.9054 (tpp) cc_final: 0.8847 (tpt) REVERT: E 158 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6287 (pp-130) REVERT: E 449 MET cc_start: 0.8735 (tpt) cc_final: 0.8374 (tpt) REVERT: E 678 MET cc_start: 0.8254 (mmm) cc_final: 0.8028 (mmm) REVERT: F 84 MET cc_start: 0.8914 (ptp) cc_final: 0.8566 (ttp) REVERT: F 158 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5793 (pp-130) REVERT: F 273 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8864 (tm-30) outliers start: 37 outliers final: 2 residues processed: 169 average time/residue: 0.7115 time to fit residues: 143.4871 Evaluate side-chains 151 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 337 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 390 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 750 ASN C 750 ASN D 750 ASN F 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.052903 restraints weight = 85150.719| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.22 r_work: 0.2610 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 35274 Z= 0.359 Angle : 0.663 11.611 47700 Z= 0.327 Chirality : 0.049 0.207 5436 Planarity : 0.005 0.046 6222 Dihedral : 9.603 151.147 5004 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.02 % Allowed : 6.41 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.84 (0.13), residues: 4338 helix: 0.67 (0.12), residues: 2070 sheet: 0.43 (0.23), residues: 588 loop : 0.72 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 377 TYR 0.006 0.001 TYR B 203 PHE 0.013 0.002 PHE A 563 TRP 0.008 0.002 TRP C 454 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00818 (35274) covalent geometry : angle 0.66298 (47700) hydrogen bonds : bond 0.04325 ( 1620) hydrogen bonds : angle 4.78000 ( 4572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.361 Fit side-chains REVERT: A 84 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7540 (pp-130) REVERT: A 158 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.5866 (pp-130) REVERT: A 678 MET cc_start: 0.8440 (mmm) cc_final: 0.8225 (mpm) REVERT: B 158 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6429 (pp-130) REVERT: B 402 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8847 (mp0) REVERT: B 449 MET cc_start: 0.8972 (tpt) cc_final: 0.8560 (tpt) REVERT: C 84 MET cc_start: 0.8967 (ptp) cc_final: 0.8671 (ppp) REVERT: C 158 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5528 (pp-130) REVERT: C 273 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 305 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8508 (mt-10) REVERT: D 84 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7534 (pp-130) REVERT: D 158 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5545 (pp-130) REVERT: D 273 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8707 (tm-30) REVERT: D 344 MET cc_start: 0.9159 (mtp) cc_final: 0.8875 (mtp) REVERT: D 678 MET cc_start: 0.8403 (mmm) cc_final: 0.8125 (mpm) REVERT: E 110 TYR cc_start: 0.8537 (m-10) cc_final: 0.8204 (m-80) REVERT: E 158 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6304 (pp-130) REVERT: E 402 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8819 (mp0) REVERT: E 449 MET cc_start: 0.8971 (tpt) cc_final: 0.8551 (tpt) REVERT: E 678 MET cc_start: 0.8212 (mmm) cc_final: 0.7848 (mmm) REVERT: F 84 MET cc_start: 0.8965 (ptp) cc_final: 0.8672 (ppp) REVERT: F 158 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5500 (pp-130) REVERT: F 273 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8883 (tm-30) REVERT: F 305 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: F 678 MET cc_start: 0.8284 (mmm) cc_final: 0.8041 (mpm) outliers start: 38 outliers final: 3 residues processed: 168 average time/residue: 0.7322 time to fit residues: 145.9724 Evaluate side-chains 152 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 155 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.091754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.055030 restraints weight = 83338.781| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.23 r_work: 0.2668 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35274 Z= 0.121 Angle : 0.513 9.964 47700 Z= 0.257 Chirality : 0.044 0.172 5436 Planarity : 0.004 0.051 6222 Dihedral : 9.657 154.033 5004 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.78 % Allowed : 8.24 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.18 (0.13), residues: 4338 helix: 1.16 (0.12), residues: 2034 sheet: 0.44 (0.23), residues: 588 loop : 0.68 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 662 TYR 0.007 0.001 TYR B 244 PHE 0.010 0.001 PHE A 302 TRP 0.006 0.001 TRP E 454 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00281 (35274) covalent geometry : angle 0.51340 (47700) hydrogen bonds : bond 0.03252 ( 1620) hydrogen bonds : angle 4.41327 ( 4572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.025 Fit side-chains REVERT: A 84 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7559 (pp-130) REVERT: A 158 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6047 (pp-130) REVERT: A 344 MET cc_start: 0.9104 (mtm) cc_final: 0.8903 (mtp) REVERT: B 158 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.5758 (pp-130) REVERT: B 402 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: C 84 MET cc_start: 0.8953 (ptp) cc_final: 0.8530 (ttp) REVERT: C 158 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5237 (pp-130) REVERT: C 273 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8735 (tm-30) REVERT: C 678 MET cc_start: 0.8579 (mmm) cc_final: 0.8297 (mpt) REVERT: D 84 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (pp-130) REVERT: D 158 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6089 (pp-130) REVERT: D 273 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8654 (tm-30) REVERT: D 292 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: E 158 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.5779 (pp-130) REVERT: E 402 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8790 (mp0) REVERT: E 449 MET cc_start: 0.8873 (tpt) cc_final: 0.8509 (tpt) REVERT: E 678 MET cc_start: 0.8272 (mmm) cc_final: 0.7718 (mmm) REVERT: F 84 MET cc_start: 0.8975 (ptp) cc_final: 0.8681 (ppp) REVERT: F 158 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5202 (pp-130) REVERT: F 273 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8732 (tm-30) outliers start: 29 outliers final: 2 residues processed: 158 average time/residue: 0.7155 time to fit residues: 134.7482 Evaluate side-chains 149 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 50 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 chunk 82 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054395 restraints weight = 83778.152| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.18 r_work: 0.2651 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 35274 Z= 0.200 Angle : 0.543 9.230 47700 Z= 0.269 Chirality : 0.045 0.164 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.560 153.906 5004 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.67 % Allowed : 8.75 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.34 (0.13), residues: 4338 helix: 1.31 (0.12), residues: 2040 sheet: 0.45 (0.23), residues: 588 loop : 0.75 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.006 0.001 TYR D 517 PHE 0.013 0.001 PHE B 674 TRP 0.006 0.001 TRP F 454 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00463 (35274) covalent geometry : angle 0.54281 (47700) hydrogen bonds : bond 0.03390 ( 1620) hydrogen bonds : angle 4.33776 ( 4572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 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: 25 poor density : 148 time to evaluate : 1.205 Fit side-chains REVERT: A 158 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.5735 (pp-130) REVERT: A 678 MET cc_start: 0.8725 (mmt) cc_final: 0.8508 (mpt) REVERT: B 158 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.5893 (pp-130) REVERT: B 678 MET cc_start: 0.8571 (mpt) cc_final: 0.8359 (mpt) REVERT: B 742 PHE cc_start: 0.9313 (m-10) cc_final: 0.9071 (m-10) REVERT: C 84 MET cc_start: 0.8913 (ptp) cc_final: 0.8431 (ppp) REVERT: C 158 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5123 (pp-130) REVERT: C 273 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 402 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8672 (mm-30) REVERT: C 678 MET cc_start: 0.8657 (mmm) cc_final: 0.8238 (mpm) REVERT: D 158 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5507 (pp-130) REVERT: D 273 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8621 (tm-30) REVERT: D 332 MET cc_start: 0.9460 (tpp) cc_final: 0.9231 (mtp) REVERT: D 678 MET cc_start: 0.8694 (mmt) cc_final: 0.8493 (mpt) REVERT: E 158 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.5689 (pp-130) REVERT: E 678 MET cc_start: 0.8413 (mmm) cc_final: 0.7955 (mmp) REVERT: F 84 MET cc_start: 0.8911 (ptp) cc_final: 0.8581 (ptp) REVERT: F 158 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5114 (pp-130) REVERT: F 273 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8766 (tm-30) REVERT: F 402 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8663 (mm-30) REVERT: F 678 MET cc_start: 0.8570 (mmm) cc_final: 0.8262 (mpm) outliers start: 25 outliers final: 2 residues processed: 159 average time/residue: 0.7249 time to fit residues: 137.6516 Evaluate side-chains 147 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 43 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.090083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053237 restraints weight = 84296.364| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.24 r_work: 0.2627 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 35274 Z= 0.247 Angle : 0.573 9.596 47700 Z= 0.283 Chirality : 0.046 0.161 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.572 155.151 5004 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.05 % Allowed : 8.72 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.35 (0.13), residues: 4338 helix: 1.35 (0.12), residues: 2040 sheet: 0.23 (0.22), residues: 648 loop : 0.82 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 377 TYR 0.007 0.001 TYR D 517 PHE 0.013 0.001 PHE A 302 TRP 0.007 0.002 TRP F 454 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00568 (35274) covalent geometry : angle 0.57319 (47700) hydrogen bonds : bond 0.03487 ( 1620) hydrogen bonds : angle 4.34096 ( 4572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.195 Fit side-chains REVERT: A 158 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6123 (pp-130) REVERT: A 678 MET cc_start: 0.8766 (mmt) cc_final: 0.8461 (mpm) REVERT: B 158 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5854 (pp-130) REVERT: B 678 MET cc_start: 0.8518 (mpt) cc_final: 0.8252 (mpt) REVERT: B 742 PHE cc_start: 0.9331 (m-10) cc_final: 0.9084 (m-10) REVERT: C 84 MET cc_start: 0.8919 (ptp) cc_final: 0.8444 (ppp) REVERT: C 158 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5193 (pp-130) REVERT: C 273 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 678 MET cc_start: 0.8747 (mmm) cc_final: 0.8360 (mpt) REVERT: D 158 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5903 (pp-130) REVERT: D 273 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8694 (tm-30) REVERT: D 678 MET cc_start: 0.8754 (mmt) cc_final: 0.8450 (mpm) REVERT: E 158 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.5719 (pp-130) REVERT: E 449 MET cc_start: 0.8974 (tpt) cc_final: 0.8546 (tpt) REVERT: E 678 MET cc_start: 0.8658 (mmm) cc_final: 0.8287 (mmm) REVERT: F 84 MET cc_start: 0.8913 (ptp) cc_final: 0.8445 (ppp) REVERT: F 158 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5172 (pp-130) REVERT: F 273 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8774 (tm-30) REVERT: F 678 MET cc_start: 0.8634 (mmm) cc_final: 0.8234 (mpm) outliers start: 39 outliers final: 12 residues processed: 171 average time/residue: 0.6443 time to fit residues: 133.5125 Evaluate side-chains 158 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 171 optimal weight: 2.9990 chunk 405 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 348 optimal weight: 0.0770 chunk 318 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 431 optimal weight: 3.9990 chunk 156 optimal weight: 30.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.090234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053392 restraints weight = 84509.418| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.25 r_work: 0.2632 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 35274 Z= 0.221 Angle : 0.557 9.289 47700 Z= 0.275 Chirality : 0.046 0.154 5436 Planarity : 0.004 0.057 6222 Dihedral : 9.583 156.623 5004 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.10 % Allowed : 8.88 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.42 (0.13), residues: 4338 helix: 1.40 (0.12), residues: 2040 sheet: 0.25 (0.22), residues: 648 loop : 0.88 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 653 TYR 0.006 0.001 TYR A 517 PHE 0.012 0.001 PHE A 302 TRP 0.007 0.001 TRP F 454 HIS 0.003 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00508 (35274) covalent geometry : angle 0.55687 (47700) hydrogen bonds : bond 0.03339 ( 1620) hydrogen bonds : angle 4.27307 ( 4572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5774 (pp-130) REVERT: A 332 MET cc_start: 0.9387 (mtp) cc_final: 0.9126 (mtp) REVERT: A 678 MET cc_start: 0.8772 (mmt) cc_final: 0.8408 (mpm) REVERT: B 158 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5844 (pp-130) REVERT: B 402 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: B 449 MET cc_start: 0.8972 (tpt) cc_final: 0.8541 (tpt) REVERT: B 742 PHE cc_start: 0.9324 (m-10) cc_final: 0.9063 (m-10) REVERT: C 84 MET cc_start: 0.8914 (ptp) cc_final: 0.8496 (ppp) REVERT: C 158 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5209 (pp-130) REVERT: C 273 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 678 MET cc_start: 0.8798 (mmm) cc_final: 0.8473 (mmm) REVERT: D 158 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5867 (pp-130) REVERT: D 273 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8696 (tm-30) REVERT: D 332 MET cc_start: 0.9391 (mtp) cc_final: 0.9133 (mtp) REVERT: D 678 MET cc_start: 0.8779 (mmt) cc_final: 0.8415 (mpm) REVERT: E 158 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5870 (pp-130) REVERT: E 402 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: E 449 MET cc_start: 0.8960 (tpt) cc_final: 0.8531 (tpt) REVERT: E 678 MET cc_start: 0.8716 (mmm) cc_final: 0.8343 (mmm) REVERT: E 742 PHE cc_start: 0.9320 (m-10) cc_final: 0.9058 (m-10) REVERT: F 84 MET cc_start: 0.8915 (ptp) cc_final: 0.8501 (ppp) REVERT: F 158 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.5197 (pp-130) REVERT: F 273 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8741 (tm-30) REVERT: F 678 MET cc_start: 0.8704 (mmm) cc_final: 0.8238 (mpm) outliers start: 41 outliers final: 12 residues processed: 171 average time/residue: 0.6445 time to fit residues: 133.5387 Evaluate side-chains 165 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 245 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 423 optimal weight: 0.9990 chunk 413 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.090823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053998 restraints weight = 84037.068| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.25 r_work: 0.2651 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35274 Z= 0.154 Angle : 0.530 8.565 47700 Z= 0.263 Chirality : 0.045 0.179 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.592 156.989 5004 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.81 % Allowed : 9.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 4338 helix: 1.49 (0.12), residues: 2040 sheet: 0.28 (0.22), residues: 648 loop : 0.90 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 653 TYR 0.006 0.001 TYR E 244 PHE 0.014 0.001 PHE A 302 TRP 0.006 0.001 TRP A 454 HIS 0.002 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00357 (35274) covalent geometry : angle 0.53008 (47700) hydrogen bonds : bond 0.03132 ( 1620) hydrogen bonds : angle 4.16934 ( 4572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.6022 (pp-130) REVERT: A 678 MET cc_start: 0.8783 (mmt) cc_final: 0.8462 (mpm) REVERT: B 84 MET cc_start: 0.8740 (ttp) cc_final: 0.8126 (ppp) REVERT: B 158 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.5834 (pp-130) REVERT: B 219 MET cc_start: 0.8914 (mtt) cc_final: 0.8652 (ttm) REVERT: B 449 MET cc_start: 0.8930 (tpt) cc_final: 0.8522 (tpt) REVERT: B 742 PHE cc_start: 0.9290 (m-10) cc_final: 0.9068 (m-10) REVERT: C 84 MET cc_start: 0.8924 (ptp) cc_final: 0.8500 (ppp) REVERT: C 158 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5115 (pp-130) REVERT: C 273 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8729 (tm-30) REVERT: C 678 MET cc_start: 0.8777 (mmm) cc_final: 0.8405 (mmm) REVERT: D 158 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5782 (pp-130) REVERT: D 273 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8665 (tm-30) REVERT: D 332 MET cc_start: 0.9383 (mtp) cc_final: 0.9100 (mtp) REVERT: D 678 MET cc_start: 0.8792 (mmt) cc_final: 0.8470 (mpm) REVERT: E 84 MET cc_start: 0.8773 (ttp) cc_final: 0.8200 (ppp) REVERT: E 158 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5813 (pp-130) REVERT: E 219 MET cc_start: 0.8917 (mtt) cc_final: 0.8654 (ttm) REVERT: E 449 MET cc_start: 0.8919 (tpt) cc_final: 0.8516 (tpt) REVERT: E 678 MET cc_start: 0.8732 (mmm) cc_final: 0.8301 (mmm) REVERT: E 742 PHE cc_start: 0.9297 (m-10) cc_final: 0.9069 (m-10) REVERT: F 84 MET cc_start: 0.8920 (ptp) cc_final: 0.8498 (ppp) REVERT: F 158 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5140 (pp-130) REVERT: F 273 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8739 (tm-30) REVERT: F 678 MET cc_start: 0.8727 (mmm) cc_final: 0.8341 (mpm) outliers start: 30 outliers final: 11 residues processed: 163 average time/residue: 0.6389 time to fit residues: 126.6476 Evaluate side-chains 163 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 152 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 400 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 378 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052359 restraints weight = 84420.880| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.25 r_work: 0.2611 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 35274 Z= 0.308 Angle : 0.625 10.097 47700 Z= 0.305 Chirality : 0.048 0.215 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.589 157.227 5004 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.72 % Allowed : 9.42 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.44 (0.13), residues: 4338 helix: 1.40 (0.12), residues: 2040 sheet: 0.23 (0.22), residues: 648 loop : 0.93 (0.17), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 653 TYR 0.007 0.001 TYR A 517 PHE 0.014 0.002 PHE B 674 TRP 0.007 0.002 TRP F 454 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00706 (35274) covalent geometry : angle 0.62458 (47700) hydrogen bonds : bond 0.03621 ( 1620) hydrogen bonds : angle 4.32736 ( 4572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5768 (pp-130) REVERT: A 678 MET cc_start: 0.8810 (mmt) cc_final: 0.8460 (mpm) REVERT: B 84 MET cc_start: 0.8748 (ttp) cc_final: 0.8079 (ppp) REVERT: B 158 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5864 (pp-130) REVERT: B 219 MET cc_start: 0.8969 (mtt) cc_final: 0.8720 (mtm) REVERT: B 402 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: B 449 MET cc_start: 0.8999 (tpt) cc_final: 0.8583 (tpt) REVERT: B 678 MET cc_start: 0.8450 (mtm) cc_final: 0.8230 (mpt) REVERT: B 742 PHE cc_start: 0.9294 (m-10) cc_final: 0.9035 (m-10) REVERT: C 84 MET cc_start: 0.8938 (ptp) cc_final: 0.8508 (ppp) REVERT: C 158 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5169 (pp-130) REVERT: C 273 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8757 (tm-30) REVERT: C 742 PHE cc_start: 0.9201 (m-10) cc_final: 0.8995 (m-80) REVERT: D 158 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5813 (pp-130) REVERT: D 273 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8701 (tm-30) REVERT: D 678 MET cc_start: 0.8814 (mmt) cc_final: 0.8467 (mpm) REVERT: E 84 MET cc_start: 0.8753 (ttp) cc_final: 0.8089 (ppp) REVERT: E 158 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.5867 (pp-130) REVERT: E 219 MET cc_start: 0.8976 (mtt) cc_final: 0.8728 (mtm) REVERT: E 402 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: E 449 MET cc_start: 0.8986 (tpt) cc_final: 0.8573 (tpt) REVERT: E 678 MET cc_start: 0.8861 (mmm) cc_final: 0.8467 (mmm) REVERT: E 742 PHE cc_start: 0.9292 (m-10) cc_final: 0.9046 (m-10) REVERT: F 84 MET cc_start: 0.8931 (ptp) cc_final: 0.8504 (ppp) REVERT: F 158 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5156 (pp-130) REVERT: F 273 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8759 (tm-30) REVERT: F 678 MET cc_start: 0.8746 (mmm) cc_final: 0.8326 (mpm) outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 0.6437 time to fit residues: 124.3750 Evaluate side-chains 167 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 118 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 357 optimal weight: 0.8980 chunk 407 optimal weight: 4.9990 chunk 378 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 436 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.091116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054809 restraints weight = 83476.446| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.19 r_work: 0.2669 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35274 Z= 0.117 Angle : 0.519 8.111 47700 Z= 0.258 Chirality : 0.044 0.175 5436 Planarity : 0.004 0.045 6222 Dihedral : 9.631 158.406 5004 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.67 % Allowed : 9.45 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4338 helix: 1.54 (0.12), residues: 2040 sheet: 0.27 (0.22), residues: 648 loop : 0.95 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 653 TYR 0.008 0.001 TYR B 244 PHE 0.014 0.001 PHE A 302 TRP 0.006 0.001 TRP A 454 HIS 0.002 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00275 (35274) covalent geometry : angle 0.51885 (47700) hydrogen bonds : bond 0.02976 ( 1620) hydrogen bonds : angle 4.11161 ( 4572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5617 (pp-130) REVERT: A 678 MET cc_start: 0.8848 (mmt) cc_final: 0.8485 (mpm) REVERT: B 84 MET cc_start: 0.8735 (ttp) cc_final: 0.8084 (ppp) REVERT: B 158 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.5871 (pp-130) REVERT: B 292 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8661 (mm-30) REVERT: B 316 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 402 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (mp0) REVERT: B 449 MET cc_start: 0.8899 (tpt) cc_final: 0.8544 (tpt) REVERT: B 742 PHE cc_start: 0.9267 (m-10) cc_final: 0.9049 (m-10) REVERT: C 84 MET cc_start: 0.8927 (ptp) cc_final: 0.8512 (ppp) REVERT: C 158 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.4963 (pp-130) REVERT: C 273 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8704 (tm-30) REVERT: C 678 MET cc_start: 0.8801 (mmm) cc_final: 0.8411 (mpm) REVERT: D 158 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5675 (pp-130) REVERT: D 273 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: D 678 MET cc_start: 0.8865 (mmt) cc_final: 0.8502 (mpm) REVERT: E 84 MET cc_start: 0.8731 (ttp) cc_final: 0.8089 (ppp) REVERT: E 158 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.5856 (pp-130) REVERT: E 292 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: E 402 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8712 (mp0) REVERT: E 449 MET cc_start: 0.8890 (tpt) cc_final: 0.8494 (tpt) REVERT: E 678 MET cc_start: 0.8801 (mmm) cc_final: 0.8379 (mmm) REVERT: E 742 PHE cc_start: 0.9287 (m-10) cc_final: 0.9055 (m-10) REVERT: F 84 MET cc_start: 0.8928 (ptp) cc_final: 0.8515 (ppp) REVERT: F 158 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.4959 (pp-130) REVERT: F 273 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8711 (tm-30) REVERT: F 678 MET cc_start: 0.8755 (mmm) cc_final: 0.8338 (mpm) outliers start: 25 outliers final: 10 residues processed: 168 average time/residue: 0.6592 time to fit residues: 134.1763 Evaluate side-chains 170 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 351 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 321 optimal weight: 0.6980 chunk 352 optimal weight: 0.6980 chunk 381 optimal weight: 0.9980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN D 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.054850 restraints weight = 83413.682| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.24 r_work: 0.2679 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35274 Z= 0.108 Angle : 0.511 8.820 47700 Z= 0.253 Chirality : 0.044 0.185 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.543 157.112 5004 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.62 % Allowed : 9.69 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.65 (0.13), residues: 4338 helix: 1.62 (0.12), residues: 2040 sheet: 0.41 (0.22), residues: 630 loop : 0.92 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 487 TYR 0.006 0.001 TYR B 244 PHE 0.016 0.001 PHE B 674 TRP 0.006 0.001 TRP C 454 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00252 (35274) covalent geometry : angle 0.51143 (47700) hydrogen bonds : bond 0.02884 ( 1620) hydrogen bonds : angle 4.02605 ( 4572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9043.18 seconds wall clock time: 154 minutes 59.27 seconds (9299.27 seconds total)