Starting phenix.real_space_refine on Sat Aug 8 02:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2026/8jyu_36731.cif" } resolution = 2.19 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= 0.002 sd= 0.176 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 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16374 2.51 5 N 4266 2.21 5 O 4782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.83, per 1000 atoms: 0.19 Number of scatterers: 25542 At special positions: 0 Unit cell: (162.75, 154.38, 95.79, 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 108 16.00 P 6 15.00 Mg 6 11.99 O 4782 8.00 N 4266 7.00 C 16374 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.0 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 39.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 removed outlier: 3.640A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.878A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.699A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS E 283 " --> pdb=" O PRO E 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 321 through 324 removed outlier: 4.328A pdb=" N GLY E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU E 338 " --> pdb=" O PRO E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS E 508 " --> pdb=" O ALA E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS F 283 " --> pdb=" O PRO F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY F 324 " --> pdb=" O SER F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU F 338 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS F 508 " --> pdb=" O ALA F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE A 433 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 463 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.616A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.478A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE D 433 " --> pdb=" O GLU D 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 461 through 463 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE B 433 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 463 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.617A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE C 433 " --> pdb=" O GLU C 436 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 461 through 463 Processing sheet with id=AC7, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE E 433 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 461 through 463 Processing sheet with id=AD4, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE F 433 " --> pdb=" O GLU F 436 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 461 through 463 948 hydrogen bonds defined for protein. 2682 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: 4.16 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4321 1.31 - 1.44: 6695 1.44 - 1.56: 14904 1.56 - 1.69: 6 1.69 - 1.81: 192 Bond restraints: 26118 Sorted by residual: bond pdb=" CA PHE C 81 " pdb=" C PHE C 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.26e+01 bond pdb=" CA PHE D 81 " pdb=" C PHE D 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.26e+01 bond pdb=" CA PHE B 81 " pdb=" C PHE B 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.25e+01 bond pdb=" CA PHE E 81 " pdb=" C PHE E 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.23e+01 bond pdb=" CA PHE A 81 " pdb=" C PHE A 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.22e+01 ... (remaining 26113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 34817 2.16 - 4.31: 478 4.31 - 6.47: 108 6.47 - 8.63: 15 8.63 - 10.78: 6 Bond angle restraints: 35424 Sorted by residual: angle pdb=" N TYR B 249 " pdb=" CA TYR B 249 " pdb=" C TYR B 249 " ideal model delta sigma weight residual 109.15 119.93 -10.78 1.44e+00 4.82e-01 5.61e+01 angle pdb=" N TYR C 249 " pdb=" CA TYR C 249 " pdb=" C TYR C 249 " ideal model delta sigma weight residual 109.15 119.92 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N TYR E 249 " pdb=" CA TYR E 249 " pdb=" C TYR E 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.59e+01 angle pdb=" N TYR D 249 " pdb=" CA TYR D 249 " pdb=" C TYR D 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" N TYR A 249 " pdb=" CA TYR A 249 " pdb=" C TYR A 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 ... (remaining 35419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14324 17.94 - 35.89: 949 35.89 - 53.83: 267 53.83 - 71.78: 60 71.78 - 89.72: 36 Dihedral angle restraints: 15636 sinusoidal: 6366 harmonic: 9270 Sorted by residual: dihedral pdb=" CA PRO F 325 " pdb=" C PRO F 325 " pdb=" N ILE F 326 " pdb=" CA ILE F 326 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO D 325 " pdb=" C PRO D 325 " pdb=" N ILE D 326 " pdb=" CA ILE D 326 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO A 325 " pdb=" C PRO A 325 " pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3530 0.079 - 0.159: 454 0.159 - 0.238: 0 0.238 - 0.317: 0 0.317 - 0.396: 18 Chirality restraints: 4002 Sorted by residual: chirality pdb=" CA PHE C 81 " pdb=" N PHE C 81 " pdb=" C PHE C 81 " pdb=" CB PHE C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA PHE E 81 " pdb=" N PHE E 81 " pdb=" C PHE E 81 " pdb=" CB PHE E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE D 81 " pdb=" N PHE D 81 " pdb=" C PHE D 81 " pdb=" CB PHE D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 3999 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 78 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU C 78 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU C 78 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS C 79 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU B 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS B 79 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C GLU D 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU D 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS D 79 " 0.018 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4101 2.76 - 3.30: 24752 3.30 - 3.83: 45681 3.83 - 4.37: 57715 4.37 - 4.90: 93277 Nonbonded interactions: 225526 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O2P AMP F 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2P AMP B 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2P AMP D 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.230 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.230 2.170 ... (remaining 225521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.160 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.004 0.062 26124 Z= 0.253 Angle : 0.658 10.784 35424 Z= 0.394 Chirality : 0.050 0.396 4002 Planarity : 0.004 0.039 4494 Dihedral : 14.446 89.722 9672 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.32 % Favored : 95.49 % Rotamer: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.10 (0.15), residues: 3168 helix: 1.25 (0.17), residues: 1050 sheet: 0.03 (0.21), residues: 576 loop : -0.72 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 529 TYR 0.012 0.001 TYR B 80 PHE 0.011 0.001 PHE C 161 TRP 0.008 0.001 TRP C 386 HIS 0.002 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.25 (26118) covalent geometry : angle 0.65773 / 0.39 (35424) hydrogen bonds : bond 0.19172 / 12.92 ( 948) hydrogen bonds : angle 7.51129 / 5.22 ( 2682) Misc. bond : bond 0.00044 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 406 time to evaluate : 0.827 Fit side-chains REVERT: A 28 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6695 (mp0) REVERT: A 42 LYS cc_start: 0.7118 (ttpp) cc_final: 0.6734 (ttpp) REVERT: A 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5971 (mmtm) REVERT: A 100 GLU cc_start: 0.6435 (tp30) cc_final: 0.5923 (tp30) REVERT: A 112 ASP cc_start: 0.7812 (m-30) cc_final: 0.7608 (m-30) REVERT: A 145 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5259 (mp0) REVERT: A 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6127 (mtm-85) REVERT: A 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7080 (mp0) REVERT: A 160 ASN cc_start: 0.7479 (m-40) cc_final: 0.7261 (m-40) REVERT: A 197 MET cc_start: 0.7883 (mmp) cc_final: 0.6507 (mtp) REVERT: A 256 ASN cc_start: 0.7290 (t0) cc_final: 0.6905 (t0) REVERT: A 285 MET cc_start: 0.7144 (mtp) cc_final: 0.6935 (mtp) REVERT: A 309 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 343 GLN cc_start: 0.7059 (mt0) cc_final: 0.6560 (mt0) REVERT: A 366 ASP cc_start: 0.5427 (m-30) cc_final: 0.5180 (m-30) REVERT: A 399 LYS cc_start: 0.6883 (ttmm) cc_final: 0.5926 (tmmt) REVERT: A 461 MET cc_start: 0.3195 (OUTLIER) cc_final: 0.2213 (mpp) REVERT: D 42 LYS cc_start: 0.6930 (ttpp) cc_final: 0.6608 (ttpp) REVERT: D 61 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6003 (mmtt) REVERT: D 100 GLU cc_start: 0.6353 (tp30) cc_final: 0.5283 (mp0) REVERT: D 118 GLU cc_start: 0.7106 (pt0) cc_final: 0.6493 (pp20) REVERT: D 145 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5200 (mp0) REVERT: D 150 ARG cc_start: 0.6432 (mtm110) cc_final: 0.6204 (mtm-85) REVERT: D 158 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6308 (tm-30) REVERT: D 160 ASN cc_start: 0.7300 (m-40) cc_final: 0.7023 (m-40) REVERT: D 197 MET cc_start: 0.7804 (mmp) cc_final: 0.6427 (mtm) REVERT: D 248 LYS cc_start: 0.7494 (tttp) cc_final: 0.7211 (tttm) REVERT: D 262 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6858 (mptt) REVERT: D 285 MET cc_start: 0.6924 (mtp) cc_final: 0.6617 (mtp) REVERT: D 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7486 (mt0) REVERT: D 346 GLU cc_start: 0.6990 (tp30) cc_final: 0.6757 (tp30) REVERT: D 399 LYS cc_start: 0.6912 (ttmm) cc_final: 0.6095 (tmmt) REVERT: D 403 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7219 (ttp80) REVERT: D 461 MET cc_start: 0.2999 (ppp) cc_final: 0.2436 (mpp) REVERT: B 42 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6730 (ttpp) REVERT: B 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5969 (mmtm) REVERT: B 100 GLU cc_start: 0.6359 (tp30) cc_final: 0.6112 (tp30) REVERT: B 112 ASP cc_start: 0.7769 (m-30) cc_final: 0.7568 (m-30) REVERT: B 145 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5290 (mp0) REVERT: B 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6131 (mtm-85) REVERT: B 158 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7079 (mp0) REVERT: B 160 ASN cc_start: 0.7481 (m-40) cc_final: 0.7265 (m-40) REVERT: B 197 MET cc_start: 0.7840 (mmp) cc_final: 0.6488 (mtp) REVERT: B 248 LYS cc_start: 0.7512 (tttp) cc_final: 0.7214 (tttm) REVERT: B 256 ASN cc_start: 0.7278 (t0) cc_final: 0.6860 (t0) REVERT: B 285 MET cc_start: 0.7151 (mtp) cc_final: 0.6932 (mtp) REVERT: B 309 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6712 (mt-10) REVERT: B 343 GLN cc_start: 0.7052 (mt0) cc_final: 0.6566 (mt0) REVERT: B 366 ASP cc_start: 0.5447 (m-30) cc_final: 0.5196 (m-30) REVERT: B 399 LYS cc_start: 0.6900 (ttmm) cc_final: 0.5952 (tmmt) REVERT: B 461 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.2095 (mpp) REVERT: C 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6489 (mp0) REVERT: C 42 LYS cc_start: 0.7042 (ttpp) cc_final: 0.6740 (tmtp) REVERT: C 61 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6153 (mmtm) REVERT: C 100 GLU cc_start: 0.6519 (tp30) cc_final: 0.5294 (mp0) REVERT: C 118 GLU cc_start: 0.7061 (pt0) cc_final: 0.6409 (pp20) REVERT: C 136 ARG cc_start: 0.7739 (ttt180) cc_final: 0.7352 (tpt-90) REVERT: C 145 GLU cc_start: 0.5648 (mm-30) cc_final: 0.5208 (mp0) REVERT: C 150 ARG cc_start: 0.6272 (mtm110) cc_final: 0.5894 (mtm110) REVERT: C 151 LEU cc_start: 0.7668 (mt) cc_final: 0.7410 (mt) REVERT: C 158 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7035 (mp0) REVERT: C 165 ASP cc_start: 0.7933 (t0) cc_final: 0.7681 (t0) REVERT: C 197 MET cc_start: 0.7712 (mmp) cc_final: 0.6705 (mtp) REVERT: C 248 LYS cc_start: 0.7605 (tttp) cc_final: 0.7339 (tttm) REVERT: C 274 HIS cc_start: 0.7553 (t70) cc_final: 0.7296 (t70) REVERT: C 309 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6834 (mt-10) REVERT: C 335 GLU cc_start: 0.5675 (mp0) cc_final: 0.5393 (tm-30) REVERT: C 343 GLN cc_start: 0.6730 (mt0) cc_final: 0.6127 (mt0) REVERT: C 344 GLN cc_start: 0.7892 (mt0) cc_final: 0.7431 (mt0) REVERT: C 366 ASP cc_start: 0.5334 (m-30) cc_final: 0.5116 (m-30) REVERT: C 399 LYS cc_start: 0.6771 (ttmm) cc_final: 0.5792 (tmmt) REVERT: C 403 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7274 (tmm160) REVERT: C 461 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2014 (mmt) REVERT: E 42 LYS cc_start: 0.6934 (ttpp) cc_final: 0.6603 (ttpp) REVERT: E 61 LYS cc_start: 0.7067 (mtmm) cc_final: 0.6050 (mmtt) REVERT: E 100 GLU cc_start: 0.6358 (tp30) cc_final: 0.5289 (mp0) REVERT: E 118 GLU cc_start: 0.7093 (pt0) cc_final: 0.6482 (pp20) REVERT: E 145 GLU cc_start: 0.5587 (mm-30) cc_final: 0.5167 (mp0) REVERT: E 150 ARG cc_start: 0.6404 (mtm110) cc_final: 0.6175 (mtm-85) REVERT: E 158 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6310 (tm-30) REVERT: E 160 ASN cc_start: 0.7306 (m-40) cc_final: 0.7040 (m-40) REVERT: E 197 MET cc_start: 0.7827 (mmp) cc_final: 0.6436 (mtm) REVERT: E 248 LYS cc_start: 0.7485 (tttp) cc_final: 0.7198 (tttm) REVERT: E 285 MET cc_start: 0.6889 (mtp) cc_final: 0.6588 (mtp) REVERT: E 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7493 (mt0) REVERT: E 346 GLU cc_start: 0.6992 (tp30) cc_final: 0.6756 (tp30) REVERT: E 399 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6160 (tmmt) REVERT: E 403 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: E 461 MET cc_start: 0.3019 (ppp) cc_final: 0.2427 (mpp) REVERT: F 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6490 (mp0) REVERT: F 42 LYS cc_start: 0.7039 (ttpp) cc_final: 0.6737 (tmtp) REVERT: F 61 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6156 (mmtm) REVERT: F 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5292 (mp0) REVERT: F 118 GLU cc_start: 0.7066 (pt0) cc_final: 0.6411 (pp20) REVERT: F 136 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7375 (tpt-90) REVERT: F 145 GLU cc_start: 0.5565 (mm-30) cc_final: 0.5147 (mp0) REVERT: F 150 ARG cc_start: 0.6271 (mtm110) cc_final: 0.5890 (mtm110) REVERT: F 151 LEU cc_start: 0.7669 (mt) cc_final: 0.7418 (mt) REVERT: F 158 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7035 (mp0) REVERT: F 165 ASP cc_start: 0.7930 (t0) cc_final: 0.7689 (t0) REVERT: F 197 MET cc_start: 0.7697 (mmp) cc_final: 0.6681 (mtp) REVERT: F 248 LYS cc_start: 0.7599 (tttp) cc_final: 0.7330 (tttm) REVERT: F 274 HIS cc_start: 0.7545 (t70) cc_final: 0.7314 (t70) REVERT: F 309 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6840 (mt-10) REVERT: F 335 GLU cc_start: 0.5703 (mp0) cc_final: 0.5401 (tm-30) REVERT: F 343 GLN cc_start: 0.6659 (mt0) cc_final: 0.6056 (mt0) REVERT: F 344 GLN cc_start: 0.7877 (mt0) cc_final: 0.7424 (mt0) REVERT: F 366 ASP cc_start: 0.5399 (m-30) cc_final: 0.5174 (m-30) REVERT: F 399 LYS cc_start: 0.6767 (ttmm) cc_final: 0.5787 (tmmt) REVERT: F 403 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7271 (tmm160) REVERT: F 461 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.2014 (mmt) outliers start: 4 outliers final: 0 residues processed: 406 average time/residue: 0.7345 time to fit residues: 337.0209 Evaluate side-chains 351 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN A 226 HIS A 344 GLN A 532 HIS D 226 HIS D 395 ASN D 532 HIS B 206 ASN B 226 HIS B 344 GLN B 532 HIS C 206 ASN C 226 HIS C 532 HIS E 226 HIS E 395 ASN E 532 HIS F 206 ASN F 226 HIS F 532 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.198427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127830 restraints weight = 17097.428| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.61 r_work: 0.3135 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26124 Z= 0.218 Angle : 0.718 9.193 35424 Z= 0.377 Chirality : 0.051 0.222 4002 Planarity : 0.005 0.037 4494 Dihedral : 7.361 59.227 3534 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.23 % Allowed : 8.08 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.16 (0.15), residues: 3168 helix: 0.73 (0.15), residues: 1104 sheet: -0.41 (0.21), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.029 0.003 TYR A 245 PHE 0.023 0.003 PHE F 81 TRP 0.016 0.002 TRP C 402 HIS 0.007 0.002 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (26118) covalent geometry : angle 0.71813 / 0.38 (35424) hydrogen bonds : bond 0.06729 / 4.52 ( 948) hydrogen bonds : angle 6.47873 / 4.50 ( 2682) Misc. bond : bond 0.00312 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 331 time to evaluate : 0.816 Fit side-chains REVERT: A 42 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8200 (ttpp) REVERT: A 61 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7413 (mmtm) REVERT: A 112 ASP cc_start: 0.8499 (m-30) cc_final: 0.8243 (m-30) REVERT: A 145 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6532 (mp0) REVERT: A 158 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7952 (mp0) REVERT: A 197 MET cc_start: 0.8928 (mmp) cc_final: 0.8144 (mtp) REVERT: A 256 ASN cc_start: 0.8098 (t0) cc_final: 0.7799 (t0) REVERT: A 309 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 335 GLU cc_start: 0.6561 (mp0) cc_final: 0.6096 (tm-30) REVERT: A 343 GLN cc_start: 0.7750 (mt0) cc_final: 0.7456 (mt0) REVERT: A 375 GLU cc_start: 0.7082 (pt0) cc_final: 0.6760 (pm20) REVERT: A 399 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7370 (tmmt) REVERT: D 61 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7462 (mmtt) REVERT: D 89 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8608 (mttt) REVERT: D 100 GLU cc_start: 0.7957 (tp30) cc_final: 0.7200 (mp0) REVERT: D 158 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7449 (tm-30) REVERT: D 197 MET cc_start: 0.8876 (mmp) cc_final: 0.8122 (mtp) REVERT: D 285 MET cc_start: 0.7473 (mtp) cc_final: 0.7133 (mtp) REVERT: D 338 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6252 (mm-30) REVERT: D 346 GLU cc_start: 0.7802 (tp30) cc_final: 0.7508 (tp30) REVERT: D 375 GLU cc_start: 0.7084 (pt0) cc_final: 0.6705 (pm20) REVERT: D 399 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7434 (tmmt) REVERT: B 61 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7411 (mmtm) REVERT: B 112 ASP cc_start: 0.8506 (m-30) cc_final: 0.8250 (m-30) REVERT: B 144 GLU cc_start: 0.6665 (pm20) cc_final: 0.6342 (pm20) REVERT: B 158 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7947 (mp0) REVERT: B 197 MET cc_start: 0.8925 (mmp) cc_final: 0.8141 (mtp) REVERT: B 256 ASN cc_start: 0.8104 (t0) cc_final: 0.7802 (t0) REVERT: B 309 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 335 GLU cc_start: 0.6557 (mp0) cc_final: 0.6119 (tm-30) REVERT: B 343 GLN cc_start: 0.7744 (mt0) cc_final: 0.7437 (mt0) REVERT: B 375 GLU cc_start: 0.7045 (pt0) cc_final: 0.6704 (pm20) REVERT: B 399 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7385 (tmmt) REVERT: C 28 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7431 (mp0) REVERT: C 61 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7524 (mmtm) REVERT: C 100 GLU cc_start: 0.8014 (tp30) cc_final: 0.7225 (mp0) REVERT: C 133 THR cc_start: 0.6327 (OUTLIER) cc_final: 0.6052 (t) REVERT: C 136 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8167 (tpt-90) REVERT: C 145 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6403 (mp0) REVERT: C 150 ARG cc_start: 0.7384 (mtm110) cc_final: 0.6981 (mtm110) REVERT: C 158 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7902 (mp0) REVERT: C 197 MET cc_start: 0.8985 (mmp) cc_final: 0.8189 (mtp) REVERT: C 248 LYS cc_start: 0.8408 (tttp) cc_final: 0.8200 (tttm) REVERT: C 274 HIS cc_start: 0.8095 (t70) cc_final: 0.7871 (t70) REVERT: C 283 LYS cc_start: 0.7338 (mmtm) cc_final: 0.7131 (mppt) REVERT: C 338 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6271 (mm-30) REVERT: C 343 GLN cc_start: 0.7506 (mt0) cc_final: 0.7091 (mt0) REVERT: C 375 GLU cc_start: 0.6991 (pt0) cc_final: 0.6612 (pm20) REVERT: C 399 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7220 (tmmt) REVERT: E 61 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7469 (mmtt) REVERT: E 89 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8610 (mttt) REVERT: E 100 GLU cc_start: 0.7928 (tp30) cc_final: 0.7191 (mp0) REVERT: E 158 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7522 (tm-30) REVERT: E 197 MET cc_start: 0.8889 (mmp) cc_final: 0.8131 (mtp) REVERT: E 285 MET cc_start: 0.7480 (mtp) cc_final: 0.7178 (mtp) REVERT: E 338 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6267 (mm-30) REVERT: E 346 GLU cc_start: 0.7799 (tp30) cc_final: 0.7506 (tp30) REVERT: E 375 GLU cc_start: 0.7061 (pt0) cc_final: 0.6693 (pm20) REVERT: E 399 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7419 (tmmt) REVERT: F 28 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7437 (mp0) REVERT: F 61 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7518 (mmtm) REVERT: F 100 GLU cc_start: 0.8010 (tp30) cc_final: 0.7221 (mp0) REVERT: F 133 THR cc_start: 0.6328 (OUTLIER) cc_final: 0.6053 (t) REVERT: F 136 ARG cc_start: 0.8455 (ttt180) cc_final: 0.8163 (tpt-90) REVERT: F 145 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6420 (mp0) REVERT: F 150 ARG cc_start: 0.7379 (mtm110) cc_final: 0.6975 (mtm110) REVERT: F 158 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7916 (mp0) REVERT: F 197 MET cc_start: 0.8988 (mmp) cc_final: 0.8194 (mtp) REVERT: F 248 LYS cc_start: 0.8404 (tttp) cc_final: 0.8194 (tttm) REVERT: F 274 HIS cc_start: 0.8105 (t70) cc_final: 0.7879 (t70) REVERT: F 283 LYS cc_start: 0.7348 (mmtm) cc_final: 0.7141 (mppt) REVERT: F 338 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6292 (mm-30) REVERT: F 343 GLN cc_start: 0.7500 (mt0) cc_final: 0.7066 (mt0) REVERT: F 375 GLU cc_start: 0.6978 (pt0) cc_final: 0.6604 (pm20) REVERT: F 399 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7214 (tmmt) outliers start: 34 outliers final: 22 residues processed: 357 average time/residue: 0.6846 time to fit residues: 277.0996 Evaluate side-chains 335 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 118 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN D 343 GLN D 344 GLN D 368 ASN B 154 GLN B 368 ASN C 154 GLN C 160 ASN C 368 ASN E 343 GLN E 344 GLN E 368 ASN F 154 GLN F 368 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.206350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165584 restraints weight = 17483.175| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 0.77 r_work: 0.3464 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 26124 Z= 0.116 Angle : 0.578 7.613 35424 Z= 0.303 Chirality : 0.045 0.191 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.901 56.536 3534 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.60 % Favored : 96.21 % Rotamer: Outliers : 1.62 % Allowed : 8.95 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.03 (0.15), residues: 3168 helix: 0.98 (0.16), residues: 1104 sheet: -0.38 (0.21), residues: 576 loop : -0.54 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 47 TYR 0.015 0.001 TYR A 245 PHE 0.017 0.001 PHE F 81 TRP 0.009 0.001 TRP C 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (26118) covalent geometry : angle 0.57834 / 0.30 (35424) hydrogen bonds : bond 0.04826 / 3.23 ( 948) hydrogen bonds : angle 5.90363 / 4.09 ( 2682) Misc. bond : bond 0.00105 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 0.689 Fit side-chains REVERT: A 61 LYS cc_start: 0.8426 (mtmm) cc_final: 0.7876 (mmtm) REVERT: A 112 ASP cc_start: 0.8726 (m-30) cc_final: 0.8455 (m-30) REVERT: A 145 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7151 (mp0) REVERT: A 197 MET cc_start: 0.9040 (mmp) cc_final: 0.8443 (mtp) REVERT: A 309 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 335 GLU cc_start: 0.6863 (mp0) cc_final: 0.6591 (tm-30) REVERT: A 343 GLN cc_start: 0.8168 (mt0) cc_final: 0.7925 (mt0) REVERT: A 399 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7851 (tmmt) REVERT: D 61 LYS cc_start: 0.8531 (mtmm) cc_final: 0.7978 (mmtm) REVERT: D 89 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8661 (ttmm) REVERT: D 100 GLU cc_start: 0.8519 (tp30) cc_final: 0.7875 (mp0) REVERT: D 158 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7975 (tm-30) REVERT: D 197 MET cc_start: 0.9011 (mmp) cc_final: 0.8350 (mtp) REVERT: D 285 MET cc_start: 0.7763 (mtp) cc_final: 0.7516 (mtp) REVERT: D 338 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6767 (mm-30) REVERT: D 399 LYS cc_start: 0.8336 (ttmm) cc_final: 0.7960 (tmmt) REVERT: B 61 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7877 (mmtm) REVERT: B 112 ASP cc_start: 0.8726 (m-30) cc_final: 0.8453 (m-30) REVERT: B 197 MET cc_start: 0.9035 (mmp) cc_final: 0.8437 (mtp) REVERT: B 309 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 335 GLU cc_start: 0.6882 (mp0) cc_final: 0.6585 (tm-30) REVERT: B 343 GLN cc_start: 0.8181 (mt0) cc_final: 0.7934 (mt0) REVERT: B 399 LYS cc_start: 0.8361 (ttmm) cc_final: 0.7870 (tmmt) REVERT: C 61 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7950 (mmtm) REVERT: C 100 GLU cc_start: 0.8457 (tp30) cc_final: 0.7872 (mp0) REVERT: C 145 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7033 (mp0) REVERT: C 150 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7561 (mtm110) REVERT: C 197 MET cc_start: 0.9072 (mmp) cc_final: 0.8453 (mtp) REVERT: C 338 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6811 (mm-30) REVERT: C 343 GLN cc_start: 0.7996 (mt0) cc_final: 0.7651 (mt0) REVERT: C 344 GLN cc_start: 0.8614 (mt0) cc_final: 0.8279 (mt0) REVERT: C 365 GLU cc_start: 0.7147 (mp0) cc_final: 0.6485 (pm20) REVERT: C 375 GLU cc_start: 0.7182 (pt0) cc_final: 0.6854 (pm20) REVERT: C 399 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7792 (tmmt) REVERT: E 61 LYS cc_start: 0.8524 (mtmm) cc_final: 0.7974 (mmtm) REVERT: E 89 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8664 (ttmm) REVERT: E 100 GLU cc_start: 0.8520 (tp30) cc_final: 0.7868 (mp0) REVERT: E 158 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7976 (tm-30) REVERT: E 197 MET cc_start: 0.9015 (mmp) cc_final: 0.8385 (mtp) REVERT: E 285 MET cc_start: 0.7758 (mtp) cc_final: 0.7507 (mtp) REVERT: E 338 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6778 (mm-30) REVERT: E 346 GLU cc_start: 0.8357 (tp30) cc_final: 0.8156 (tp30) REVERT: E 399 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7926 (tmmt) REVERT: F 61 LYS cc_start: 0.8526 (mtmm) cc_final: 0.7980 (mmtm) REVERT: F 100 GLU cc_start: 0.8420 (tp30) cc_final: 0.7856 (mp0) REVERT: F 145 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7033 (mp0) REVERT: F 150 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7552 (mtm110) REVERT: F 197 MET cc_start: 0.9078 (mmp) cc_final: 0.8461 (mtp) REVERT: F 338 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6853 (mm-30) REVERT: F 343 GLN cc_start: 0.8016 (mt0) cc_final: 0.7713 (mt0) REVERT: F 344 GLN cc_start: 0.8606 (mt0) cc_final: 0.8280 (mt0) REVERT: F 365 GLU cc_start: 0.7149 (mp0) cc_final: 0.6490 (pm20) REVERT: F 375 GLU cc_start: 0.7185 (pt0) cc_final: 0.6853 (pm20) REVERT: F 399 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7785 (tmmt) outliers start: 45 outliers final: 20 residues processed: 360 average time/residue: 0.6505 time to fit residues: 266.6961 Evaluate side-chains 314 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 294 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 313 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 GLN B 126 GLN C 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.199771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129423 restraints weight = 17185.970| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.49 r_work: 0.3150 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26124 Z= 0.154 Angle : 0.628 8.495 35424 Z= 0.329 Chirality : 0.047 0.200 4002 Planarity : 0.004 0.037 4494 Dihedral : 7.193 59.594 3534 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.70 % Allowed : 9.09 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.09 (0.15), residues: 3168 helix: 0.92 (0.16), residues: 1104 sheet: -0.45 (0.21), residues: 576 loop : -0.56 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.020 0.002 TYR B 245 PHE 0.020 0.002 PHE F 81 TRP 0.010 0.001 TRP C 402 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (26118) covalent geometry : angle 0.62812 / 0.33 (35424) hydrogen bonds : bond 0.05552 / 3.72 ( 948) hydrogen bonds : angle 6.02979 / 4.18 ( 2682) Misc. bond : bond 0.00255 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 0.650 Fit side-chains REVERT: A 61 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7467 (mmtm) REVERT: A 112 ASP cc_start: 0.8517 (m-30) cc_final: 0.8246 (m-30) REVERT: A 144 GLU cc_start: 0.6607 (pm20) cc_final: 0.6266 (pm20) REVERT: A 197 MET cc_start: 0.8994 (mmp) cc_final: 0.8248 (mtp) REVERT: A 335 GLU cc_start: 0.6646 (mp0) cc_final: 0.6146 (tm-30) REVERT: A 343 GLN cc_start: 0.7771 (mt0) cc_final: 0.7474 (mt0) REVERT: A 366 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: A 375 GLU cc_start: 0.7208 (pt0) cc_final: 0.6854 (pm20) REVERT: A 399 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7451 (tmmt) REVERT: D 61 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7567 (mmtm) REVERT: D 89 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8613 (ttmm) REVERT: D 100 GLU cc_start: 0.8058 (tp30) cc_final: 0.7338 (mp0) REVERT: D 158 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7614 (tm-30) REVERT: D 197 MET cc_start: 0.8933 (mmp) cc_final: 0.8186 (mtp) REVERT: D 285 MET cc_start: 0.7528 (mtp) cc_final: 0.7255 (mtp) REVERT: D 338 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6242 (mm-30) REVERT: D 399 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7558 (tmmt) REVERT: B 61 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7471 (mmtm) REVERT: B 197 MET cc_start: 0.8992 (mmp) cc_final: 0.8244 (mtp) REVERT: B 309 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 335 GLU cc_start: 0.6642 (mp0) cc_final: 0.6146 (tm-30) REVERT: B 343 GLN cc_start: 0.7779 (mt0) cc_final: 0.7477 (mt0) REVERT: B 366 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: B 375 GLU cc_start: 0.7209 (pt0) cc_final: 0.6858 (pm20) REVERT: B 399 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7465 (tmmt) REVERT: C 42 LYS cc_start: 0.8353 (tmtp) cc_final: 0.8003 (ttpp) REVERT: C 61 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7588 (mmtm) REVERT: C 100 GLU cc_start: 0.8005 (tp30) cc_final: 0.7294 (mp0) REVERT: C 145 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6426 (mp0) REVERT: C 150 ARG cc_start: 0.7349 (mtm110) cc_final: 0.7058 (mtm110) REVERT: C 197 MET cc_start: 0.9016 (mmp) cc_final: 0.8261 (mtp) REVERT: C 338 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6274 (mm-30) REVERT: C 343 GLN cc_start: 0.7563 (mt0) cc_final: 0.7142 (mt0) REVERT: C 375 GLU cc_start: 0.7123 (pt0) cc_final: 0.6710 (pm20) REVERT: C 399 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7395 (tmmt) REVERT: E 61 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7568 (mmtm) REVERT: E 89 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8612 (ttmm) REVERT: E 100 GLU cc_start: 0.8053 (tp30) cc_final: 0.7327 (mp0) REVERT: E 158 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7616 (tm-30) REVERT: E 197 MET cc_start: 0.8935 (mmp) cc_final: 0.8184 (mtp) REVERT: E 248 LYS cc_start: 0.8354 (tttm) cc_final: 0.8141 (tttm) REVERT: E 285 MET cc_start: 0.7555 (mtp) cc_final: 0.7274 (mtp) REVERT: E 338 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6244 (mm-30) REVERT: E 346 GLU cc_start: 0.7880 (tp30) cc_final: 0.7603 (tp30) REVERT: E 399 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7550 (tmmt) REVERT: F 42 LYS cc_start: 0.8356 (tmtp) cc_final: 0.8010 (ttpp) REVERT: F 61 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7588 (mmtm) REVERT: F 100 GLU cc_start: 0.8001 (tp30) cc_final: 0.7296 (mp0) REVERT: F 145 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6425 (mp0) REVERT: F 150 ARG cc_start: 0.7350 (mtm110) cc_final: 0.7061 (mtm110) REVERT: F 197 MET cc_start: 0.9017 (mmp) cc_final: 0.8260 (mtp) REVERT: F 283 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7171 (mppt) REVERT: F 335 GLU cc_start: 0.6724 (mp0) cc_final: 0.6239 (tm-30) REVERT: F 338 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6264 (mm-30) REVERT: F 343 GLN cc_start: 0.7535 (mt0) cc_final: 0.7121 (mt0) REVERT: F 375 GLU cc_start: 0.7127 (pt0) cc_final: 0.6711 (pm20) REVERT: F 399 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7366 (tmmt) outliers start: 47 outliers final: 40 residues processed: 339 average time/residue: 0.6507 time to fit residues: 252.8045 Evaluate side-chains 339 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 183 optimal weight: 0.0030 chunk 279 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 70 optimal weight: 0.0570 chunk 270 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 overall best weight: 2.9512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 GLN C 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.198192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127160 restraints weight = 17008.638| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.64 r_work: 0.3135 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26124 Z= 0.213 Angle : 0.709 9.262 35424 Z= 0.370 Chirality : 0.050 0.213 4002 Planarity : 0.005 0.039 4494 Dihedral : 7.475 59.024 3534 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 1.91 % Allowed : 9.02 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.27 (0.15), residues: 3168 helix: 0.68 (0.15), residues: 1104 sheet: -0.58 (0.21), residues: 576 loop : -0.57 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 47 TYR 0.026 0.003 TYR B 245 PHE 0.026 0.003 PHE F 81 TRP 0.013 0.002 TRP A 402 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (26118) covalent geometry : angle 0.70887 / 0.37 (35424) hydrogen bonds : bond 0.06413 / 4.32 ( 948) hydrogen bonds : angle 6.27457 / 4.35 ( 2682) Misc. bond : bond 0.00438 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 1.109 Fit side-chains REVERT: A 61 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7388 (mmtm) REVERT: A 144 GLU cc_start: 0.6589 (pm20) cc_final: 0.6213 (pm20) REVERT: A 197 MET cc_start: 0.8925 (mmp) cc_final: 0.8130 (mtp) REVERT: A 335 GLU cc_start: 0.6625 (mp0) cc_final: 0.5967 (tm-30) REVERT: A 343 GLN cc_start: 0.7733 (mt0) cc_final: 0.7437 (mt0) REVERT: A 366 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: A 375 GLU cc_start: 0.7130 (pt0) cc_final: 0.6803 (pm20) REVERT: A 399 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7375 (tmmt) REVERT: D 61 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7422 (mmtt) REVERT: D 89 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8572 (mttt) REVERT: D 100 GLU cc_start: 0.7963 (tp30) cc_final: 0.7181 (mp0) REVERT: D 158 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7440 (tm-30) REVERT: D 197 MET cc_start: 0.8878 (mmp) cc_final: 0.8062 (mtp) REVERT: D 262 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7960 (mmmt) REVERT: D 285 MET cc_start: 0.7541 (mtp) cc_final: 0.7201 (mtp) REVERT: D 335 GLU cc_start: 0.6601 (mp0) cc_final: 0.6120 (tm-30) REVERT: D 338 GLU cc_start: 0.6907 (mt-10) cc_final: 0.5955 (mm-30) REVERT: D 366 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: D 375 GLU cc_start: 0.7039 (pt0) cc_final: 0.6668 (pm20) REVERT: D 399 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7426 (tmmt) REVERT: B 61 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7394 (mmtm) REVERT: B 144 GLU cc_start: 0.6607 (pm20) cc_final: 0.6224 (pm20) REVERT: B 197 MET cc_start: 0.8919 (mmp) cc_final: 0.8120 (mtp) REVERT: B 335 GLU cc_start: 0.6612 (mp0) cc_final: 0.5974 (tm-30) REVERT: B 343 GLN cc_start: 0.7729 (mt0) cc_final: 0.7427 (mt0) REVERT: B 366 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: B 375 GLU cc_start: 0.7139 (pt0) cc_final: 0.6811 (pm20) REVERT: B 399 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7378 (tmmt) REVERT: C 42 LYS cc_start: 0.8287 (tmtp) cc_final: 0.7895 (ttpp) REVERT: C 61 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7469 (mmtm) REVERT: C 100 GLU cc_start: 0.7884 (tp30) cc_final: 0.7118 (mp0) REVERT: C 150 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6838 (mtm110) REVERT: C 197 MET cc_start: 0.8962 (mmp) cc_final: 0.8149 (mtp) REVERT: C 283 LYS cc_start: 0.7337 (mmtm) cc_final: 0.6969 (mppt) REVERT: C 335 GLU cc_start: 0.6673 (mp0) cc_final: 0.6053 (tm-30) REVERT: C 338 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6034 (mm-30) REVERT: C 343 GLN cc_start: 0.7465 (mt0) cc_final: 0.7066 (mt0) REVERT: C 375 GLU cc_start: 0.7057 (pt0) cc_final: 0.6683 (pm20) REVERT: C 399 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7235 (tmmt) REVERT: E 61 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7442 (mmtt) REVERT: E 89 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8578 (mttt) REVERT: E 100 GLU cc_start: 0.7904 (tp30) cc_final: 0.7135 (mp0) REVERT: E 158 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7439 (tm-30) REVERT: E 197 MET cc_start: 0.8876 (mmp) cc_final: 0.8057 (mtp) REVERT: E 262 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7957 (mmmt) REVERT: E 285 MET cc_start: 0.7536 (mtp) cc_final: 0.7201 (mtp) REVERT: E 335 GLU cc_start: 0.6606 (mp0) cc_final: 0.6120 (tm-30) REVERT: E 338 GLU cc_start: 0.6914 (mt-10) cc_final: 0.5961 (mm-30) REVERT: E 346 GLU cc_start: 0.7683 (tp30) cc_final: 0.7377 (tp30) REVERT: E 366 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6501 (m-30) REVERT: E 375 GLU cc_start: 0.7039 (pt0) cc_final: 0.6668 (pm20) REVERT: E 399 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7414 (tmmt) REVERT: F 42 LYS cc_start: 0.8297 (tmtp) cc_final: 0.7905 (ttpp) REVERT: F 61 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7467 (mmtm) REVERT: F 100 GLU cc_start: 0.7878 (tp30) cc_final: 0.7116 (mp0) REVERT: F 150 ARG cc_start: 0.7252 (mtm110) cc_final: 0.6843 (mtm110) REVERT: F 197 MET cc_start: 0.8964 (mmp) cc_final: 0.8150 (mtp) REVERT: F 283 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6965 (mppt) REVERT: F 335 GLU cc_start: 0.6654 (mp0) cc_final: 0.6047 (tm-30) REVERT: F 338 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6031 (mm-30) REVERT: F 343 GLN cc_start: 0.7452 (mt0) cc_final: 0.6987 (mt0) REVERT: F 375 GLU cc_start: 0.6992 (pt0) cc_final: 0.6612 (pm20) REVERT: F 399 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7226 (tmmt) outliers start: 53 outliers final: 37 residues processed: 339 average time/residue: 0.7273 time to fit residues: 281.4859 Evaluate side-chains 336 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN D 343 GLN E 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.199780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129218 restraints weight = 17222.811| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.38 r_work: 0.3189 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26124 Z= 0.147 Angle : 0.621 8.078 35424 Z= 0.325 Chirality : 0.047 0.203 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.174 59.123 3534 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.66 % Allowed : 9.42 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.08 (0.15), residues: 3168 helix: 0.86 (0.16), residues: 1104 sheet: -0.39 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.021 0.002 TYR A 245 PHE 0.021 0.002 PHE B 81 TRP 0.011 0.001 TRP A 402 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (26118) covalent geometry : angle 0.62115 / 0.33 (35424) hydrogen bonds : bond 0.05377 / 3.61 ( 948) hydrogen bonds : angle 5.94423 / 4.12 ( 2682) Misc. bond : bond 0.00243 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 1.060 Fit side-chains REVERT: A 61 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7425 (mmtm) REVERT: A 112 ASP cc_start: 0.8444 (m-30) cc_final: 0.8165 (m-30) REVERT: A 197 MET cc_start: 0.8920 (mmp) cc_final: 0.8140 (mtp) REVERT: A 335 GLU cc_start: 0.6652 (mp0) cc_final: 0.6091 (tm-30) REVERT: A 343 GLN cc_start: 0.7748 (mt0) cc_final: 0.7461 (mt0) REVERT: A 375 GLU cc_start: 0.7166 (pt0) cc_final: 0.6833 (pm20) REVERT: A 399 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7434 (tmmt) REVERT: D 61 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7486 (mmtm) REVERT: D 89 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8499 (ttmm) REVERT: D 100 GLU cc_start: 0.7952 (tp30) cc_final: 0.7234 (mp0) REVERT: D 158 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7496 (tm-30) REVERT: D 197 MET cc_start: 0.8881 (mmp) cc_final: 0.8082 (mtp) REVERT: D 262 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7902 (mmmt) REVERT: D 285 MET cc_start: 0.7514 (mtp) cc_final: 0.7184 (mtp) REVERT: D 335 GLU cc_start: 0.6724 (mp0) cc_final: 0.6276 (tm-30) REVERT: D 338 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6059 (mm-30) REVERT: D 375 GLU cc_start: 0.7068 (pt0) cc_final: 0.6715 (pm20) REVERT: D 399 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7466 (tmmt) REVERT: B 61 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7434 (mmtm) REVERT: B 112 ASP cc_start: 0.8451 (m-30) cc_final: 0.8173 (m-30) REVERT: B 197 MET cc_start: 0.8911 (mmp) cc_final: 0.8129 (mtp) REVERT: B 335 GLU cc_start: 0.6631 (mp0) cc_final: 0.6087 (tm-30) REVERT: B 343 GLN cc_start: 0.7765 (mt0) cc_final: 0.7458 (mt0) REVERT: B 375 GLU cc_start: 0.7153 (pt0) cc_final: 0.6823 (pm20) REVERT: B 399 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7436 (tmmt) REVERT: C 42 LYS cc_start: 0.8290 (tmtp) cc_final: 0.7929 (ttpp) REVERT: C 61 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7531 (mmtm) REVERT: C 100 GLU cc_start: 0.7917 (tp30) cc_final: 0.7207 (mp0) REVERT: C 150 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6940 (mtm110) REVERT: C 197 MET cc_start: 0.8959 (mmp) cc_final: 0.8175 (mtp) REVERT: C 283 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7135 (mppt) REVERT: C 335 GLU cc_start: 0.6729 (mp0) cc_final: 0.6180 (tm-30) REVERT: C 338 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6239 (mm-30) REVERT: C 343 GLN cc_start: 0.7483 (mt0) cc_final: 0.7113 (mt0) REVERT: C 375 GLU cc_start: 0.7078 (pt0) cc_final: 0.6705 (pm20) REVERT: C 399 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7311 (tmmt) REVERT: C 461 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.1809 (mtt) REVERT: E 61 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7481 (mmtm) REVERT: E 89 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8503 (ttmm) REVERT: E 100 GLU cc_start: 0.7942 (tp30) cc_final: 0.7225 (mp0) REVERT: E 158 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7499 (tm-30) REVERT: E 197 MET cc_start: 0.8884 (mmp) cc_final: 0.8083 (mtp) REVERT: E 248 LYS cc_start: 0.8410 (tttm) cc_final: 0.8201 (tttm) REVERT: E 262 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7912 (mmmt) REVERT: E 285 MET cc_start: 0.7526 (mtp) cc_final: 0.7195 (mtp) REVERT: E 335 GLU cc_start: 0.6727 (mp0) cc_final: 0.6262 (tm-30) REVERT: E 338 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6049 (mm-30) REVERT: E 346 GLU cc_start: 0.7757 (tp30) cc_final: 0.7521 (tp30) REVERT: E 375 GLU cc_start: 0.7049 (pt0) cc_final: 0.6713 (pm20) REVERT: E 399 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7461 (tmmt) REVERT: F 61 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7526 (mmtm) REVERT: F 100 GLU cc_start: 0.7914 (tp30) cc_final: 0.7209 (mp0) REVERT: F 150 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6939 (mtm110) REVERT: F 197 MET cc_start: 0.8965 (mmp) cc_final: 0.8178 (mtp) REVERT: F 283 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7136 (mppt) REVERT: F 335 GLU cc_start: 0.6726 (mp0) cc_final: 0.6183 (tm-30) REVERT: F 338 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6237 (mm-30) REVERT: F 343 GLN cc_start: 0.7492 (mt0) cc_final: 0.7045 (mt0) REVERT: F 375 GLU cc_start: 0.7073 (pt0) cc_final: 0.6700 (pm20) REVERT: F 399 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7311 (tmmt) REVERT: F 461 MET cc_start: 0.2489 (OUTLIER) cc_final: 0.1824 (mtt) outliers start: 46 outliers final: 39 residues processed: 341 average time/residue: 0.7115 time to fit residues: 278.1964 Evaluate side-chains 338 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 242 optimal weight: 0.0270 chunk 230 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 297 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 GLN C 126 GLN C 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.206955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.163052 restraints weight = 17312.357| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 0.79 r_work: 0.3445 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26124 Z= 0.111 Angle : 0.565 7.668 35424 Z= 0.297 Chirality : 0.045 0.180 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.820 57.720 3534 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.70 % Allowed : 9.52 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.04 (0.15), residues: 3168 helix: 0.99 (0.16), residues: 1122 sheet: -0.31 (0.22), residues: 546 loop : -0.50 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.013 0.001 TYR A 245 PHE 0.017 0.001 PHE B 81 TRP 0.009 0.001 TRP E 402 HIS 0.003 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (26118) covalent geometry : angle 0.56526 / 0.30 (35424) hydrogen bonds : bond 0.04444 / 2.97 ( 948) hydrogen bonds : angle 5.61067 / 3.88 ( 2682) Misc. bond : bond 0.00124 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 1.019 Fit side-chains REVERT: A 61 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7643 (mmtm) REVERT: A 112 ASP cc_start: 0.8632 (m-30) cc_final: 0.8363 (m-30) REVERT: A 197 MET cc_start: 0.9012 (mmp) cc_final: 0.8380 (mtp) REVERT: A 335 GLU cc_start: 0.6979 (mp0) cc_final: 0.6443 (tm-30) REVERT: A 343 GLN cc_start: 0.8096 (mt0) cc_final: 0.7838 (mt0) REVERT: A 399 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7807 (tmmt) REVERT: D 61 LYS cc_start: 0.8467 (mtmm) cc_final: 0.7815 (mmtm) REVERT: D 89 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8693 (ttmm) REVERT: D 100 GLU cc_start: 0.8433 (tp30) cc_final: 0.7693 (mp0) REVERT: D 158 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7778 (tm-30) REVERT: D 197 MET cc_start: 0.8963 (mmp) cc_final: 0.8292 (mtp) REVERT: D 285 MET cc_start: 0.7529 (mtp) cc_final: 0.7265 (mtp) REVERT: D 335 GLU cc_start: 0.7108 (mp0) cc_final: 0.6557 (tm-30) REVERT: D 338 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6390 (mm-30) REVERT: D 399 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7772 (tmmt) REVERT: D 461 MET cc_start: 0.2342 (OUTLIER) cc_final: 0.1955 (mpp) REVERT: B 61 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7632 (mmtm) REVERT: B 112 ASP cc_start: 0.8634 (m-30) cc_final: 0.8364 (m-30) REVERT: B 197 MET cc_start: 0.9007 (mmp) cc_final: 0.8376 (mtp) REVERT: B 248 LYS cc_start: 0.8504 (tttm) cc_final: 0.8283 (tttp) REVERT: B 335 GLU cc_start: 0.6975 (mp0) cc_final: 0.6438 (tm-30) REVERT: B 343 GLN cc_start: 0.8091 (mt0) cc_final: 0.7831 (mt0) REVERT: B 399 LYS cc_start: 0.8427 (ttmm) cc_final: 0.7824 (tmmt) REVERT: C 61 LYS cc_start: 0.8451 (mtmm) cc_final: 0.7761 (mmtm) REVERT: C 100 GLU cc_start: 0.8395 (tp30) cc_final: 0.7697 (mp0) REVERT: C 150 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7421 (mtm110) REVERT: C 197 MET cc_start: 0.9055 (mmp) cc_final: 0.8388 (mtp) REVERT: C 283 LYS cc_start: 0.7587 (mmtm) cc_final: 0.7246 (mppt) REVERT: C 335 GLU cc_start: 0.6908 (mp0) cc_final: 0.6291 (tm-30) REVERT: C 338 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6487 (mm-30) REVERT: C 343 GLN cc_start: 0.7803 (mt0) cc_final: 0.7456 (mt0) REVERT: C 344 GLN cc_start: 0.8501 (mt0) cc_final: 0.8148 (mt0) REVERT: C 365 GLU cc_start: 0.7044 (mp0) cc_final: 0.6394 (mp0) REVERT: C 375 GLU cc_start: 0.7228 (pt0) cc_final: 0.6860 (pm20) REVERT: C 399 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7713 (tmmt) REVERT: C 461 MET cc_start: 0.2399 (OUTLIER) cc_final: 0.1620 (mtt) REVERT: E 61 LYS cc_start: 0.8463 (mtmm) cc_final: 0.7821 (mmtm) REVERT: E 89 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8717 (ttmm) REVERT: E 100 GLU cc_start: 0.8425 (tp30) cc_final: 0.7682 (mp0) REVERT: E 158 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7765 (tm-30) REVERT: E 197 MET cc_start: 0.8959 (mmp) cc_final: 0.8287 (mtp) REVERT: E 285 MET cc_start: 0.7551 (mtp) cc_final: 0.7289 (mtp) REVERT: E 335 GLU cc_start: 0.7086 (mp0) cc_final: 0.6535 (tm-30) REVERT: E 338 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6401 (mm-30) REVERT: E 346 GLU cc_start: 0.8408 (tp30) cc_final: 0.8169 (tp30) REVERT: E 399 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7763 (tmmt) REVERT: E 461 MET cc_start: 0.2298 (OUTLIER) cc_final: 0.1912 (mpp) REVERT: F 61 LYS cc_start: 0.8456 (mtmm) cc_final: 0.7780 (mmtm) REVERT: F 100 GLU cc_start: 0.8387 (tp30) cc_final: 0.7699 (mp0) REVERT: F 150 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7410 (mtm110) REVERT: F 197 MET cc_start: 0.9061 (mmp) cc_final: 0.8393 (mtp) REVERT: F 283 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7249 (mppt) REVERT: F 335 GLU cc_start: 0.6885 (mp0) cc_final: 0.6280 (tm-30) REVERT: F 338 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6478 (mm-30) REVERT: F 343 GLN cc_start: 0.7799 (mt0) cc_final: 0.7447 (mt0) REVERT: F 365 GLU cc_start: 0.7007 (mp0) cc_final: 0.6346 (mp0) REVERT: F 375 GLU cc_start: 0.7229 (pt0) cc_final: 0.6862 (pm20) REVERT: F 399 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7718 (tmmt) REVERT: F 461 MET cc_start: 0.2403 (OUTLIER) cc_final: 0.1622 (mtt) outliers start: 47 outliers final: 30 residues processed: 340 average time/residue: 0.7309 time to fit residues: 284.6188 Evaluate side-chains 324 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 146 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN F 126 GLN F 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.197156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127044 restraints weight = 17052.059| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.58 r_work: 0.3121 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26124 Z= 0.281 Angle : 0.784 9.190 35424 Z= 0.408 Chirality : 0.054 0.235 4002 Planarity : 0.005 0.044 4494 Dihedral : 7.550 59.423 3534 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.73 % Favored : 95.08 % Rotamer: Outliers : 1.88 % Allowed : 9.81 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.27 (0.14), residues: 3168 helix: 0.58 (0.15), residues: 1104 sheet: -0.55 (0.21), residues: 546 loop : -0.51 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.030 0.004 TYR B 245 PHE 0.026 0.003 PHE A 187 TRP 0.012 0.002 TRP B 402 HIS 0.006 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.28 (26118) covalent geometry : angle 0.78381 / 0.41 (35424) hydrogen bonds : bond 0.07019 / 4.73 ( 948) hydrogen bonds : angle 6.32088 / 4.38 ( 2682) Misc. bond : bond 0.00647 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 1.038 Fit side-chains REVERT: A 61 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7394 (mmtm) REVERT: A 144 GLU cc_start: 0.6537 (pm20) cc_final: 0.6168 (pm20) REVERT: A 197 MET cc_start: 0.8884 (mmp) cc_final: 0.8098 (mtp) REVERT: A 335 GLU cc_start: 0.6682 (mp0) cc_final: 0.5950 (tm-30) REVERT: A 343 GLN cc_start: 0.7748 (mt0) cc_final: 0.7446 (mt0) REVERT: A 375 GLU cc_start: 0.7143 (pt0) cc_final: 0.6780 (pm20) REVERT: A 399 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7428 (tmmt) REVERT: A 461 MET cc_start: 0.2611 (OUTLIER) cc_final: 0.1832 (mmm) REVERT: D 61 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7468 (mmtm) REVERT: D 89 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8579 (mttt) REVERT: D 100 GLU cc_start: 0.7965 (tp30) cc_final: 0.7185 (mp0) REVERT: D 158 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7428 (tm-30) REVERT: D 197 MET cc_start: 0.8828 (mmp) cc_final: 0.8068 (mtp) REVERT: D 262 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7853 (mmmt) REVERT: D 285 MET cc_start: 0.7548 (mtp) cc_final: 0.7274 (mtp) REVERT: D 335 GLU cc_start: 0.6587 (mp0) cc_final: 0.6054 (tm-30) REVERT: D 338 GLU cc_start: 0.6944 (mt-10) cc_final: 0.5948 (mm-30) REVERT: D 366 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6377 (m-30) REVERT: D 375 GLU cc_start: 0.7119 (pt0) cc_final: 0.6634 (pt0) REVERT: D 399 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7451 (tmmt) REVERT: B 61 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7401 (mmtm) REVERT: B 144 GLU cc_start: 0.6552 (pm20) cc_final: 0.6177 (pm20) REVERT: B 197 MET cc_start: 0.8878 (mmp) cc_final: 0.8093 (mtp) REVERT: B 335 GLU cc_start: 0.6690 (mp0) cc_final: 0.5962 (tm-30) REVERT: B 343 GLN cc_start: 0.7745 (mt0) cc_final: 0.7444 (mt0) REVERT: B 375 GLU cc_start: 0.7142 (pt0) cc_final: 0.6778 (pm20) REVERT: B 399 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7423 (tmmt) REVERT: C 42 LYS cc_start: 0.8291 (tmtp) cc_final: 0.7900 (ttpp) REVERT: C 61 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7464 (mmtm) REVERT: C 100 GLU cc_start: 0.7906 (tp30) cc_final: 0.7131 (mp0) REVERT: C 150 ARG cc_start: 0.7343 (mtm110) cc_final: 0.6905 (mtm110) REVERT: C 197 MET cc_start: 0.8948 (mmp) cc_final: 0.8149 (mtp) REVERT: C 283 LYS cc_start: 0.7384 (mmtm) cc_final: 0.7015 (mppt) REVERT: C 335 GLU cc_start: 0.6598 (mp0) cc_final: 0.5899 (tm-30) REVERT: C 338 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6109 (mm-30) REVERT: C 343 GLN cc_start: 0.7443 (mt0) cc_final: 0.7057 (mt0) REVERT: C 375 GLU cc_start: 0.7003 (pt0) cc_final: 0.6566 (pm20) REVERT: C 399 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7273 (tmmt) REVERT: E 61 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7419 (mmtt) REVERT: E 89 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8581 (mttt) REVERT: E 100 GLU cc_start: 0.7957 (tp30) cc_final: 0.7184 (mp0) REVERT: E 158 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7429 (tm-30) REVERT: E 197 MET cc_start: 0.8837 (mmp) cc_final: 0.8078 (mtp) REVERT: E 262 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7858 (mmmt) REVERT: E 285 MET cc_start: 0.7550 (mtp) cc_final: 0.7276 (mtp) REVERT: E 335 GLU cc_start: 0.6583 (mp0) cc_final: 0.6048 (tm-30) REVERT: E 338 GLU cc_start: 0.6940 (mt-10) cc_final: 0.5948 (mm-30) REVERT: E 346 GLU cc_start: 0.7737 (tp30) cc_final: 0.7505 (tp30) REVERT: E 366 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6436 (m-30) REVERT: E 375 GLU cc_start: 0.7105 (pt0) cc_final: 0.6620 (pt0) REVERT: E 399 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7448 (tmmt) REVERT: F 42 LYS cc_start: 0.8293 (tmtp) cc_final: 0.7901 (ttpp) REVERT: F 61 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7458 (mmtm) REVERT: F 100 GLU cc_start: 0.7904 (tp30) cc_final: 0.7119 (mp0) REVERT: F 150 ARG cc_start: 0.7349 (mtm110) cc_final: 0.6912 (mtm110) REVERT: F 197 MET cc_start: 0.8952 (mmp) cc_final: 0.8148 (mtp) REVERT: F 283 LYS cc_start: 0.7387 (mmtm) cc_final: 0.7020 (mppt) REVERT: F 335 GLU cc_start: 0.6607 (mp0) cc_final: 0.5905 (tm-30) REVERT: F 338 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6107 (mm-30) REVERT: F 343 GLN cc_start: 0.7436 (mt0) cc_final: 0.6985 (mt0) REVERT: F 375 GLU cc_start: 0.7008 (pt0) cc_final: 0.6571 (pm20) REVERT: F 399 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7271 (tmmt) outliers start: 52 outliers final: 35 residues processed: 339 average time/residue: 0.7336 time to fit residues: 284.8187 Evaluate side-chains 337 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 84 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 206 optimal weight: 40.0000 chunk 193 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 261 optimal weight: 0.0010 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 126 GLN D 154 GLN D 343 GLN C 160 ASN C 206 ASN E 154 GLN E 343 GLN F 160 ASN F 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.201591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135431 restraints weight = 17229.915| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.40 r_work: 0.3194 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26124 Z= 0.120 Angle : 0.594 8.062 35424 Z= 0.310 Chirality : 0.045 0.188 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.989 59.973 3534 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.63 % Favored : 96.18 % Rotamer: Outliers : 1.33 % Allowed : 10.35 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.06 (0.15), residues: 3168 helix: 0.89 (0.16), residues: 1116 sheet: -0.43 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.014 0.001 TYR A 245 PHE 0.019 0.001 PHE F 81 TRP 0.010 0.001 TRP E 402 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (26118) covalent geometry : angle 0.59371 / 0.31 (35424) hydrogen bonds : bond 0.04725 / 3.16 ( 948) hydrogen bonds : angle 5.73381 / 3.97 ( 2682) Misc. bond : bond 0.00137 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7476 (mmtm) REVERT: A 112 ASP cc_start: 0.8486 (m-30) cc_final: 0.8205 (m-30) REVERT: A 197 MET cc_start: 0.8940 (mmp) cc_final: 0.8215 (mtp) REVERT: A 335 GLU cc_start: 0.6855 (mp0) cc_final: 0.6292 (tm-30) REVERT: A 343 GLN cc_start: 0.7789 (mt0) cc_final: 0.7494 (mt0) REVERT: A 365 GLU cc_start: 0.7061 (mp0) cc_final: 0.6528 (mp0) REVERT: A 399 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7585 (tmmt) REVERT: D 61 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7518 (mmtm) REVERT: D 89 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8612 (ttmm) REVERT: D 100 GLU cc_start: 0.8051 (tp30) cc_final: 0.7349 (mp0) REVERT: D 158 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7615 (tm-30) REVERT: D 256 ASN cc_start: 0.7972 (t0) cc_final: 0.7724 (t0) REVERT: D 262 LYS cc_start: 0.8238 (mmtm) cc_final: 0.8012 (mmmt) REVERT: D 285 MET cc_start: 0.7507 (mtp) cc_final: 0.7218 (mtp) REVERT: D 335 GLU cc_start: 0.6788 (mp0) cc_final: 0.6354 (tm-30) REVERT: D 338 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6080 (mm-30) REVERT: D 399 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7615 (tmmt) REVERT: B 61 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7470 (mmtm) REVERT: B 112 ASP cc_start: 0.8489 (m-30) cc_final: 0.8212 (m-30) REVERT: B 197 MET cc_start: 0.8932 (mmp) cc_final: 0.8207 (mtp) REVERT: B 248 LYS cc_start: 0.8318 (tttm) cc_final: 0.8056 (tttp) REVERT: B 335 GLU cc_start: 0.6846 (mp0) cc_final: 0.6293 (tm-30) REVERT: B 343 GLN cc_start: 0.7789 (mt0) cc_final: 0.7474 (mt0) REVERT: B 365 GLU cc_start: 0.7046 (mp0) cc_final: 0.6505 (mp0) REVERT: B 399 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7581 (tmmt) REVERT: C 61 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7568 (mmtm) REVERT: C 100 GLU cc_start: 0.8039 (tp30) cc_final: 0.7321 (mp0) REVERT: C 150 ARG cc_start: 0.7331 (mtm110) cc_final: 0.7020 (mtm110) REVERT: C 197 MET cc_start: 0.8972 (mmp) cc_final: 0.8199 (mtp) REVERT: C 335 GLU cc_start: 0.6800 (mp0) cc_final: 0.6173 (tm-30) REVERT: C 338 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6170 (mm-30) REVERT: C 343 GLN cc_start: 0.7530 (mt0) cc_final: 0.7165 (mt0) REVERT: C 344 GLN cc_start: 0.8442 (mt0) cc_final: 0.7974 (mt0) REVERT: C 365 GLU cc_start: 0.6887 (mp0) cc_final: 0.6128 (mp0) REVERT: C 375 GLU cc_start: 0.7078 (pt0) cc_final: 0.6696 (pm20) REVERT: C 399 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7440 (tmmt) REVERT: C 461 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.1819 (mmm) REVERT: E 61 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7515 (mmtm) REVERT: E 89 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8618 (ttmm) REVERT: E 100 GLU cc_start: 0.8049 (tp30) cc_final: 0.7350 (mp0) REVERT: E 158 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7607 (tm-30) REVERT: E 256 ASN cc_start: 0.7975 (t0) cc_final: 0.7727 (t0) REVERT: E 262 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8019 (mmmt) REVERT: E 285 MET cc_start: 0.7522 (mtp) cc_final: 0.7234 (mtp) REVERT: E 335 GLU cc_start: 0.6786 (mp0) cc_final: 0.6339 (tm-30) REVERT: E 338 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6082 (mm-30) REVERT: E 346 GLU cc_start: 0.7784 (tp30) cc_final: 0.7581 (tp30) REVERT: E 365 GLU cc_start: 0.6970 (mp0) cc_final: 0.6353 (mp0) REVERT: E 399 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7611 (tmmt) REVERT: F 61 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7563 (mmtm) REVERT: F 100 GLU cc_start: 0.8032 (tp30) cc_final: 0.7319 (mp0) REVERT: F 150 ARG cc_start: 0.7336 (mtm110) cc_final: 0.7027 (mtm110) REVERT: F 197 MET cc_start: 0.8975 (mmp) cc_final: 0.8198 (mtp) REVERT: F 335 GLU cc_start: 0.6812 (mp0) cc_final: 0.6178 (tm-30) REVERT: F 338 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6165 (mm-30) REVERT: F 343 GLN cc_start: 0.7518 (mt0) cc_final: 0.7150 (mt0) REVERT: F 344 GLN cc_start: 0.8433 (mt0) cc_final: 0.8003 (mt0) REVERT: F 365 GLU cc_start: 0.6892 (mp0) cc_final: 0.6137 (mp0) REVERT: F 375 GLU cc_start: 0.7074 (pt0) cc_final: 0.6692 (pm20) REVERT: F 399 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7434 (tmmt) REVERT: F 461 MET cc_start: 0.2406 (OUTLIER) cc_final: 0.1712 (mmm) outliers start: 37 outliers final: 31 residues processed: 333 average time/residue: 0.7295 time to fit residues: 278.4703 Evaluate side-chains 324 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 0.4980 chunk 270 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 343 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.205870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142050 restraints weight = 17222.535| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.96 r_work: 0.3274 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26124 Z= 0.121 Angle : 0.591 7.801 35424 Z= 0.308 Chirality : 0.045 0.190 4002 Planarity : 0.004 0.037 4494 Dihedral : 6.943 59.060 3534 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 1.30 % Allowed : 10.82 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.02 (0.15), residues: 3168 helix: 1.00 (0.16), residues: 1116 sheet: -0.36 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.017 0.001 TYR B 245 PHE 0.019 0.001 PHE C 81 TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (26118) covalent geometry : angle 0.59132 / 0.31 (35424) hydrogen bonds : bond 0.04740 / 3.17 ( 948) hydrogen bonds : angle 5.66713 / 3.93 ( 2682) Misc. bond : bond 0.00172 / 0.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7602 (mmtm) REVERT: A 112 ASP cc_start: 0.8572 (m-30) cc_final: 0.8301 (m-30) REVERT: A 197 MET cc_start: 0.8973 (mmp) cc_final: 0.8272 (mtp) REVERT: A 335 GLU cc_start: 0.6768 (mp0) cc_final: 0.6294 (tm-30) REVERT: A 343 GLN cc_start: 0.7851 (mt0) cc_final: 0.7585 (mt0) REVERT: A 365 GLU cc_start: 0.7096 (mp0) cc_final: 0.6576 (mp0) REVERT: A 399 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7721 (tmmt) REVERT: D 61 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7709 (mmtm) REVERT: D 89 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8644 (ttmm) REVERT: D 100 GLU cc_start: 0.8139 (tp30) cc_final: 0.7454 (mp0) REVERT: D 158 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7755 (tm-30) REVERT: D 197 MET cc_start: 0.8969 (mmm) cc_final: 0.8150 (mtp) REVERT: D 256 ASN cc_start: 0.7981 (t0) cc_final: 0.7745 (t0) REVERT: D 285 MET cc_start: 0.7499 (mtp) cc_final: 0.7165 (mtp) REVERT: D 335 GLU cc_start: 0.6811 (mp0) cc_final: 0.6352 (tm-30) REVERT: D 338 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6113 (mm-30) REVERT: D 399 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7680 (tmmt) REVERT: B 61 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7613 (mmtm) REVERT: B 112 ASP cc_start: 0.8575 (m-30) cc_final: 0.8304 (m-30) REVERT: B 197 MET cc_start: 0.8965 (mmp) cc_final: 0.8262 (mtp) REVERT: B 248 LYS cc_start: 0.8388 (tttm) cc_final: 0.8132 (tttp) REVERT: B 335 GLU cc_start: 0.6797 (mp0) cc_final: 0.6296 (tm-30) REVERT: B 343 GLN cc_start: 0.7835 (mt0) cc_final: 0.7532 (mt0) REVERT: B 365 GLU cc_start: 0.7099 (mp0) cc_final: 0.6635 (mp0) REVERT: B 399 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7720 (tmmt) REVERT: C 42 LYS cc_start: 0.8434 (tmtp) cc_final: 0.8136 (ttpp) REVERT: C 61 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7672 (mmtm) REVERT: C 100 GLU cc_start: 0.8125 (tp30) cc_final: 0.7463 (mp0) REVERT: C 150 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7132 (mtm110) REVERT: C 197 MET cc_start: 0.9025 (mmp) cc_final: 0.8277 (mtp) REVERT: C 335 GLU cc_start: 0.6687 (mp0) cc_final: 0.6153 (tm-30) REVERT: C 338 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6293 (mm-30) REVERT: C 343 GLN cc_start: 0.7499 (mt0) cc_final: 0.7078 (mt0) REVERT: C 365 GLU cc_start: 0.6868 (mp0) cc_final: 0.6127 (mp0) REVERT: C 375 GLU cc_start: 0.7091 (pt0) cc_final: 0.6702 (pm20) REVERT: C 399 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7623 (tmmt) REVERT: E 61 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7707 (mmtm) REVERT: E 89 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8643 (ttmm) REVERT: E 100 GLU cc_start: 0.8137 (tp30) cc_final: 0.7456 (mp0) REVERT: E 158 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7762 (tm-30) REVERT: E 197 MET cc_start: 0.8974 (mmm) cc_final: 0.8156 (mtp) REVERT: E 256 ASN cc_start: 0.7983 (t0) cc_final: 0.7748 (t0) REVERT: E 285 MET cc_start: 0.7457 (mtp) cc_final: 0.7201 (mtp) REVERT: E 335 GLU cc_start: 0.6814 (mp0) cc_final: 0.6350 (tm-30) REVERT: E 338 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6142 (mm-30) REVERT: E 346 GLU cc_start: 0.7953 (tp30) cc_final: 0.7706 (tp30) REVERT: E 375 GLU cc_start: 0.7126 (pt0) cc_final: 0.6757 (pm20) REVERT: E 399 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7674 (tmmt) REVERT: F 42 LYS cc_start: 0.8436 (tmtp) cc_final: 0.8140 (ttpp) REVERT: F 61 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7680 (mmtm) REVERT: F 100 GLU cc_start: 0.8130 (tp30) cc_final: 0.7470 (mp0) REVERT: F 150 ARG cc_start: 0.7421 (mtm110) cc_final: 0.7128 (mtm110) REVERT: F 197 MET cc_start: 0.9022 (mmp) cc_final: 0.8268 (mtp) REVERT: F 335 GLU cc_start: 0.6676 (mp0) cc_final: 0.6149 (tm-30) REVERT: F 338 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6236 (mm-30) REVERT: F 343 GLN cc_start: 0.7502 (mt0) cc_final: 0.7074 (mt0) REVERT: F 365 GLU cc_start: 0.6856 (mp0) cc_final: 0.6112 (mp0) REVERT: F 375 GLU cc_start: 0.7093 (pt0) cc_final: 0.6705 (pm20) REVERT: F 399 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7617 (tmmt) REVERT: F 461 MET cc_start: 0.2538 (OUTLIER) cc_final: 0.1808 (mmm) outliers start: 36 outliers final: 34 residues processed: 328 average time/residue: 0.7038 time to fit residues: 264.6583 Evaluate side-chains 323 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 127 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 158 optimal weight: 0.2980 chunk 59 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN D 343 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.196460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124906 restraints weight = 16966.835| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.41 r_work: 0.3117 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26124 Z= 0.112 Angle : 0.575 7.566 35424 Z= 0.300 Chirality : 0.045 0.190 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.803 57.280 3534 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 1.41 % Allowed : 10.97 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.09 (0.15), residues: 3168 helix: 1.07 (0.16), residues: 1116 sheet: -0.32 (0.22), residues: 546 loop : -0.49 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.013 0.001 TYR A 245 PHE 0.018 0.001 PHE C 81 TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (26118) covalent geometry : angle 0.57520 / 0.30 (35424) hydrogen bonds : bond 0.04441 / 2.97 ( 948) hydrogen bonds : angle 5.52921 / 3.83 ( 2682) Misc. bond : bond 0.00129 / 0.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11988.95 seconds wall clock time: 204 minutes 29.36 seconds (12269.36 seconds total)