Starting phenix.real_space_refine on Mon Jul 6 10:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jy5_22521/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.map" model { file = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jy5_22521/07_2026/7jy5_22521.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.42, 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 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: 1.12 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: 9.13 Time building geometry restraints manager: 3.90 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: 21310 30.71 - 61.41: 518 61.41 - 92.12: 54 92.12 - 122.82: 6 122.82 - 153.53: 6 Dihedral angle restraints: 21894 sinusoidal: 9210 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 21891 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: 0.12 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.430 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 13.957 153.525 13638 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/Z covalent geometry : bond 0.00861 / 0.36 (35274) covalent geometry : angle 0.67162 / 0.37 (47700) hydrogen bonds : bond 0.18946 / 12.65 ( 1620) hydrogen bonds : angle 6.73216 / 4.80 ( 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 : 1.361 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: 0.8440 time to fit residues: 206.9515 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 : 1.355 ------------------------------------------------------------------------------- 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... ** 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 = 0.3699 r_free = 0.3699 target = 0.092956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.056431 restraints weight = 83197.789| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.22 r_work: 0.2690 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1298 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 : 0.577 9.117 47700 Z= 0.293 Chirality : 0.046 0.210 5436 Planarity : 0.004 0.048 6222 Dihedral : 9.002 148.789 4872 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.99 % Allowed : 4.46 % Favored : 94.55 % 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: 0.47 (0.13), residues: 4338 helix: 0.34 (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 0.004 0.001 ARG F 662 TYR 0.007 0.001 TYR D 517 PHE 0.008 0.001 PHE E 290 TRP 0.007 0.001 TRP E 454 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (35274) covalent geometry : angle 0.57693 / 0.29 (47700) hydrogen bonds : bond 0.04147 / 2.75 ( 1620) hydrogen bonds : angle 4.90596 / 3.52 ( 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 195 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.457 Fit side-chains REVERT: A 84 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7627 (pp-130) REVERT: A 158 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6008 (pp-130) REVERT: B 158 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6428 (pp-130) REVERT: B 201 VAL cc_start: 0.8959 (t) cc_final: 0.8653 (t) REVERT: B 427 MET cc_start: 0.8580 (mtp) cc_final: 0.8337 (mmm) REVERT: B 449 MET cc_start: 0.8761 (tpt) cc_final: 0.8452 (tpt) REVERT: C 84 MET cc_start: 0.8904 (ptp) cc_final: 0.8689 (ppp) REVERT: C 158 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5824 (pp-130) REVERT: C 273 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8797 (tm-30) REVERT: D 84 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7577 (pp-130) REVERT: D 158 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.5856 (pp-130) REVERT: D 273 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8468 (tp30) REVERT: E 158 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6309 (pp-130) REVERT: E 449 MET cc_start: 0.8733 (tpt) cc_final: 0.8417 (tpt) REVERT: E 678 MET cc_start: 0.8225 (mmm) cc_final: 0.8014 (mmm) REVERT: F 84 MET cc_start: 0.8902 (ptp) cc_final: 0.8689 (ppp) REVERT: F 158 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5816 (pp-130) REVERT: F 273 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8796 (tm-30) outliers start: 37 outliers final: 3 residues processed: 169 average time/residue: 0.7206 time to fit residues: 145.9931 Evaluate side-chains 151 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 A residue 757 MET 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: 10.0000 chunk 213 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 390 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 750 ASN C 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053150 restraints weight = 84787.626| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.21 r_work: 0.2615 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 35274 Z= 0.330 Angle : 0.647 11.484 47700 Z= 0.319 Chirality : 0.049 0.197 5436 Planarity : 0.005 0.058 6222 Dihedral : 8.943 149.067 4872 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 0.88 (0.13), residues: 4338 helix: 0.72 (0.12), residues: 2070 sheet: 0.42 (0.23), residues: 588 loop : 0.73 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 377 TYR 0.007 0.001 TYR E 203 PHE 0.013 0.002 PHE E 736 TRP 0.008 0.002 TRP C 454 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.33 (35274) covalent geometry : angle 0.64672 / 0.32 (47700) hydrogen bonds : bond 0.04235 / 2.83 ( 1620) hydrogen bonds : angle 4.72129 / 3.41 ( 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 : 1.494 Fit side-chains REVERT: A 84 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7555 (pp-130) REVERT: A 158 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.5869 (pp-130) REVERT: A 678 MET cc_start: 0.8440 (mmm) cc_final: 0.8221 (mpm) REVERT: B 158 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.5946 (pp-130) REVERT: B 402 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8805 (mp0) REVERT: B 449 MET cc_start: 0.8961 (tpt) cc_final: 0.8547 (tpt) REVERT: C 84 MET cc_start: 0.8966 (ptp) cc_final: 0.8671 (ppp) REVERT: C 158 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.5548 (pp-130) REVERT: C 273 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8762 (tm-30) REVERT: C 678 MET cc_start: 0.8377 (mmm) cc_final: 0.8138 (mpm) REVERT: D 84 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7570 (pp-130) REVERT: D 158 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.5639 (pp-130) REVERT: D 273 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8706 (tm-30) REVERT: E 110 TYR cc_start: 0.8540 (m-10) cc_final: 0.8206 (m-80) REVERT: E 158 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.5955 (pp-130) REVERT: E 402 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8812 (mp0) REVERT: E 449 MET cc_start: 0.8963 (tpt) cc_final: 0.8541 (tpt) REVERT: E 678 MET cc_start: 0.8197 (mmm) cc_final: 0.7832 (mmm) REVERT: F 84 MET cc_start: 0.8966 (ptp) cc_final: 0.8672 (ppp) REVERT: F 158 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5510 (pp-130) REVERT: F 273 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8764 (tm-30) REVERT: F 678 MET cc_start: 0.8353 (mmm) cc_final: 0.8115 (mpm) outliers start: 38 outliers final: 3 residues processed: 168 average time/residue: 0.8216 time to fit residues: 163.7595 Evaluate side-chains 151 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 155 optimal weight: 9.9990 chunk 404 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 235 optimal weight: 0.0470 chunk 202 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.092227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055627 restraints weight = 83047.000| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.22 r_work: 0.2680 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35274 Z= 0.105 Angle : 0.508 9.786 47700 Z= 0.254 Chirality : 0.044 0.223 5436 Planarity : 0.004 0.047 6222 Dihedral : 8.887 154.269 4872 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.81 % Allowed : 8.21 % 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: 1.12 (0.13), residues: 4338 helix: 1.19 (0.12), residues: 2034 sheet: -0.02 (0.21), residues: 678 loop : 0.76 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 653 TYR 0.007 0.001 TYR B 244 PHE 0.011 0.001 PHE A 302 TRP 0.005 0.001 TRP E 454 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (35274) covalent geometry : angle 0.50812 / 0.25 (47700) hydrogen bonds : bond 0.03179 / 2.11 ( 1620) hydrogen bonds : angle 4.37160 / 3.15 ( 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 180 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.483 Fit side-chains REVERT: A 84 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7570 (pp-130) REVERT: A 158 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6041 (pp-130) REVERT: A 678 MET cc_start: 0.8537 (mmm) cc_final: 0.8335 (mpt) REVERT: B 158 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6221 (pp-130) REVERT: B 402 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8771 (mp0) REVERT: C 84 MET cc_start: 0.8904 (ptp) cc_final: 0.8392 (ttp) REVERT: C 158 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5222 (pp-130) REVERT: C 273 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8686 (tm-30) REVERT: D 84 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7807 (pp-130) REVERT: D 158 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6061 (pp-130) REVERT: D 273 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8606 (tm-30) REVERT: D 678 MET cc_start: 0.8413 (mpm) cc_final: 0.8185 (mpt) REVERT: E 46 MET cc_start: 0.6894 (mpt) cc_final: 0.6317 (mpt) REVERT: E 158 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6254 (pp-130) REVERT: E 402 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8777 (mp0) REVERT: E 449 MET cc_start: 0.8853 (tpt) cc_final: 0.8496 (tpt) REVERT: E 678 MET cc_start: 0.8268 (mmm) cc_final: 0.7760 (mmm) REVERT: F 84 MET cc_start: 0.8905 (ptp) cc_final: 0.8395 (ttp) REVERT: F 158 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5061 (pp-130) REVERT: F 273 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8680 (tm-30) outliers start: 30 outliers final: 4 residues processed: 160 average time/residue: 0.8074 time to fit residues: 154.2320 Evaluate side-chains 151 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 B residue 201 VAL 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 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: 0.0030 chunk 164 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.090516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054139 restraints weight = 83852.753| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.20 r_work: 0.2644 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 35274 Z= 0.224 Angle : 0.551 9.346 47700 Z= 0.273 Chirality : 0.046 0.167 5436 Planarity : 0.004 0.047 6222 Dihedral : 8.864 153.902 4872 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.78 % Allowed : 8.62 % Favored : 90.61 % 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: 1.36 (0.13), residues: 4338 helix: 1.32 (0.12), residues: 2040 sheet: 0.48 (0.23), residues: 588 loop : 0.76 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.006 0.001 TYR A 517 PHE 0.017 0.001 PHE B 674 TRP 0.006 0.001 TRP B 476 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (35274) covalent geometry : angle 0.55122 / 0.27 (47700) hydrogen bonds : bond 0.03436 / 2.29 ( 1620) hydrogen bonds : angle 4.33084 / 3.12 ( 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 176 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.475 Fit side-chains REVERT: A 158 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.5930 (pp-130) REVERT: B 158 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.5901 (pp-130) REVERT: B 742 PHE cc_start: 0.9303 (m-10) cc_final: 0.9060 (m-10) REVERT: C 84 MET cc_start: 0.8929 (ptp) cc_final: 0.8448 (ppp) REVERT: C 158 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5130 (pp-130) REVERT: C 273 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8756 (tm-30) REVERT: C 402 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8675 (mm-30) REVERT: C 678 MET cc_start: 0.8575 (mmm) cc_final: 0.8267 (mpm) REVERT: D 158 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5424 (pp-130) REVERT: D 273 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8628 (tm-30) REVERT: D 332 MET cc_start: 0.9463 (tpp) cc_final: 0.9202 (mtp) REVERT: E 158 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5607 (pp-130) REVERT: E 678 MET cc_start: 0.8419 (mmm) cc_final: 0.7960 (mmp) REVERT: F 84 MET cc_start: 0.8926 (ptp) cc_final: 0.8447 (ppp) REVERT: F 158 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5108 (pp-130) REVERT: F 273 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8756 (tm-30) REVERT: F 402 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8671 (mm-30) REVERT: F 678 MET cc_start: 0.8553 (mmm) cc_final: 0.8324 (mpt) outliers start: 29 outliers final: 4 residues processed: 160 average time/residue: 0.7928 time to fit residues: 151.4118 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 : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET 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 B residue 201 VAL 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: 6.9990 chunk 265 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 255 optimal weight: 0.0170 chunk 146 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.089516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.053206 restraints weight = 83948.234| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.16 r_work: 0.2625 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 35274 Z= 0.306 Angle : 0.615 10.176 47700 Z= 0.302 Chirality : 0.048 0.221 5436 Planarity : 0.004 0.051 6222 Dihedral : 8.954 156.460 4872 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.02 % Allowed : 8.75 % 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: 1.31 (0.13), residues: 4338 helix: 1.30 (0.12), residues: 2040 sheet: 0.24 (0.22), residues: 648 loop : 0.82 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 653 TYR 0.008 0.001 TYR A 517 PHE 0.014 0.002 PHE D 302 TRP 0.007 0.002 TRP F 454 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.31 (35274) covalent geometry : angle 0.61524 / 0.30 (47700) hydrogen bonds : bond 0.03672 / 2.44 ( 1620) hydrogen bonds : angle 4.41264 / 3.18 ( 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 186 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.667 Fit side-chains REVERT: A 158 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5451 (pp-130) REVERT: A 678 MET cc_start: 0.8724 (mmt) cc_final: 0.8470 (mpt) REVERT: B 158 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.5885 (pp-130) REVERT: B 742 PHE cc_start: 0.9325 (m-10) cc_final: 0.9068 (m-10) REVERT: C 84 MET cc_start: 0.8926 (ptp) cc_final: 0.8452 (ppp) REVERT: C 158 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5219 (pp-130) REVERT: C 273 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 678 MET cc_start: 0.8639 (mmm) cc_final: 0.8265 (mpt) REVERT: D 158 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5492 (pp-130) REVERT: D 273 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8660 (tm-30) REVERT: D 678 MET cc_start: 0.8600 (mpm) cc_final: 0.8389 (mmt) REVERT: E 158 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5591 (pp-130) REVERT: E 678 MET cc_start: 0.8685 (mmm) cc_final: 0.8323 (mmm) REVERT: F 84 MET cc_start: 0.8926 (ptp) cc_final: 0.8453 (ppp) REVERT: F 158 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5216 (pp-130) REVERT: F 273 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8764 (tm-30) REVERT: F 678 MET cc_start: 0.8622 (mmm) cc_final: 0.8236 (mpm) outliers start: 38 outliers final: 14 residues processed: 171 average time/residue: 0.7100 time to fit residues: 147.5569 Evaluate side-chains 162 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 158 MET 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 201 VAL 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 292 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 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: 1.9990 chunk 405 optimal weight: 0.7980 chunk 247 optimal weight: 0.7980 chunk 348 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 431 optimal weight: 4.9990 chunk 156 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054813 restraints weight = 83403.847| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.21 r_work: 0.2666 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35274 Z= 0.120 Angle : 0.513 8.791 47700 Z= 0.257 Chirality : 0.044 0.188 5436 Planarity : 0.004 0.044 6222 Dihedral : 8.927 159.474 4872 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.94 % Allowed : 8.99 % Favored : 90.07 % 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: 1.48 (0.13), residues: 4338 helix: 1.48 (0.12), residues: 2040 sheet: 0.27 (0.22), residues: 648 loop : 0.87 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.006 0.001 TYR E 244 PHE 0.016 0.001 PHE B 674 TRP 0.007 0.001 TRP D 454 HIS 0.002 0.001 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (35274) covalent geometry : angle 0.51348 / 0.26 (47700) hydrogen bonds : bond 0.03104 / 2.06 ( 1620) hydrogen bonds : angle 4.17763 / 3.01 ( 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 179 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.6018 (pp-130) REVERT: A 678 MET cc_start: 0.8751 (mmt) cc_final: 0.8490 (mpt) REVERT: B 158 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.5751 (pp-130) REVERT: B 449 MET cc_start: 0.8917 (tpt) cc_final: 0.8517 (tpt) REVERT: B 742 PHE cc_start: 0.9297 (m-10) cc_final: 0.9048 (m-10) REVERT: C 84 MET cc_start: 0.8933 (ptp) cc_final: 0.8505 (ppp) REVERT: C 158 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5100 (pp-130) REVERT: C 273 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8720 (tm-30) REVERT: C 402 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8783 (mm-30) REVERT: C 678 MET cc_start: 0.8686 (mmm) cc_final: 0.8251 (mpt) REVERT: D 158 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5785 (pp-130) REVERT: D 273 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: D 678 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8300 (mpp) REVERT: E 158 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5754 (pp-130) REVERT: E 449 MET cc_start: 0.8910 (tpt) cc_final: 0.8562 (tpt) REVERT: E 678 MET cc_start: 0.8667 (mmm) cc_final: 0.8152 (mmp) REVERT: E 742 PHE cc_start: 0.9294 (m-10) cc_final: 0.9030 (m-10) REVERT: F 84 MET cc_start: 0.8932 (ptp) cc_final: 0.8507 (ppp) REVERT: F 158 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5108 (pp-130) REVERT: F 273 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8709 (tm-30) REVERT: F 402 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8787 (mm-30) REVERT: F 678 MET cc_start: 0.8701 (mmm) cc_final: 0.8249 (mpm) outliers start: 35 outliers final: 10 residues processed: 163 average time/residue: 0.6874 time to fit residues: 136.1567 Evaluate side-chains 161 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 158 MET 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 201 VAL Chi-restraints excluded: chain B residue 235 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 678 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3406 > 50: distance: 79 - 145: 27.120 distance: 82 - 142: 14.498 distance: 112 - 117: 22.784 distance: 117 - 118: 18.863 distance: 118 - 119: 44.065 distance: 118 - 121: 6.121 distance: 119 - 120: 49.817 distance: 119 - 123: 50.069 distance: 121 - 122: 10.598 distance: 123 - 124: 55.847 distance: 123 - 129: 40.280 distance: 124 - 125: 23.759 distance: 124 - 127: 17.487 distance: 125 - 126: 22.128 distance: 125 - 130: 8.415 distance: 127 - 128: 11.795 distance: 128 - 129: 9.315 distance: 130 - 131: 17.733 distance: 131 - 132: 6.912 distance: 131 - 134: 6.670 distance: 132 - 133: 19.781 distance: 132 - 142: 20.068 distance: 135 - 136: 12.165 distance: 135 - 137: 19.410 distance: 136 - 138: 12.015 distance: 137 - 139: 9.683 distance: 138 - 140: 19.255 distance: 139 - 140: 18.425 distance: 140 - 141: 10.916 distance: 142 - 143: 16.995 distance: 143 - 144: 34.632 distance: 143 - 146: 35.507 distance: 144 - 145: 32.640 distance: 144 - 148: 42.132 distance: 146 - 147: 8.828 distance: 148 - 149: 22.701 distance: 149 - 150: 26.595 distance: 149 - 152: 24.372 distance: 150 - 151: 26.430 distance: 150 - 156: 18.307 distance: 152 - 153: 20.222 distance: 152 - 154: 38.034 distance: 153 - 155: 16.914 distance: 156 - 157: 4.813 distance: 157 - 158: 24.838 distance: 157 - 160: 23.968 distance: 158 - 159: 7.329 distance: 158 - 163: 12.459 distance: 160 - 161: 15.579 distance: 160 - 162: 21.439 distance: 163 - 164: 9.810 distance: 164 - 165: 25.273 distance: 164 - 167: 19.039 distance: 165 - 166: 39.757 distance: 165 - 168: 38.338 distance: 168 - 169: 11.564 distance: 168 - 174: 14.416 distance: 169 - 170: 6.609 distance: 169 - 172: 7.259 distance: 170 - 171: 22.227 distance: 172 - 173: 15.595 distance: 173 - 174: 10.003 distance: 175 - 176: 18.086 distance: 176 - 177: 11.857 distance: 176 - 179: 10.760 distance: 177 - 178: 35.381 distance: 177 - 183: 14.515 distance: 179 - 180: 10.234 distance: 180 - 181: 28.463 distance: 180 - 182: 18.999 distance: 183 - 184: 30.264 distance: 184 - 185: 21.702 distance: 184 - 187: 13.629 distance: 185 - 186: 6.476 distance: 185 - 190: 20.236 distance: 187 - 189: 4.820