Starting phenix.real_space_refine on Sun Jul 5 08:00:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwg_44974/07_2026/9bwg_44974.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14795 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 100 5.16 5 C 9700 2.51 5 N 2320 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14810 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {' ZN': 2, 'PIO': 5, 'PX4': 4} Inner-chain residues flagged as termini: ['pdbres="GLY A 504 "'] Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 104 Unusual residues: {' ZN': 2, 'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 104 Unusual residues: {' ZN': 2, 'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 104 Unusual residues: {' ZN': 2, 'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 104 Unusual residues: {' ZN': 2, 'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PX4:plan-1': 3, 'PX4:plan-2': 1, 'PIO:plan-2': 5} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.89, per 1000 atoms: 0.20 Number of scatterers: 14810 At special positions: 0 Unit cell: (97.44, 99.12, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 100 16.00 O 2680 8.00 N 2320 7.00 C 9700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=1.55 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=1.55 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=1.55 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=1.55 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=1.55 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 557.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 427 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 215 " pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" ND1 HIS B 109 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 427 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 215 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" ND1 HIS C 109 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 427 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 215 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" ND1 HIS D 109 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 427 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 215 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" ND1 HIS E 109 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 427 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 215 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" ND1 HIS A 109 " 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 40.3% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.653A pdb=" N PHE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.648A pdb=" N MET A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.690A pdb=" N ILE A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 308 Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.655A pdb=" N ALA A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.652A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.648A pdb=" N MET B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.690A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 308 Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.654A pdb=" N ALA B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.654A pdb=" N PHE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.647A pdb=" N MET C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 228 removed outlier: 3.690A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 308 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.655A pdb=" N ALA C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.653A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.648A pdb=" N MET D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 228 removed outlier: 3.690A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 308 Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.654A pdb=" N ALA D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'E' and resid 9 through 18 removed outlier: 3.654A pdb=" N PHE E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.647A pdb=" N MET E 89 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 228 removed outlier: 3.690A pdb=" N ILE E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 240 Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.655A pdb=" N ALA E 392 " --> pdb=" O PHE E 388 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.753A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 120 removed outlier: 5.984A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.186A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 194 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 removed outlier: 3.501A pdb=" N GLY A 205 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.754A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 120 removed outlier: 5.983A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.186A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 211 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 189 removed outlier: 3.501A pdb=" N GLY B 205 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.752A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 116 through 120 removed outlier: 5.984A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.186A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 194 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 187 through 189 removed outlier: 3.502A pdb=" N GLY C 205 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.753A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 120 removed outlier: 5.983A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.186A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP D 194 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 189 removed outlier: 3.501A pdb=" N GLY D 205 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.752A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 116 through 120 removed outlier: 5.983A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.186A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 211 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP E 194 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 187 through 189 removed outlier: 3.501A pdb=" N GLY E 205 " --> pdb=" O TYR E 202 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2250 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: 2.05 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2290 1.31 - 1.44: 4170 1.44 - 1.57: 8365 1.57 - 1.69: 110 1.69 - 1.82: 165 Bond restraints: 15100 Sorted by residual: bond pdb=" C23 PX4 E 611 " pdb=" O7 PX4 E 611 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C23 PX4 C 508 " pdb=" O7 PX4 C 508 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C23 PX4 B 509 " pdb=" O7 PX4 B 509 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C23 PX4 B 508 " pdb=" O7 PX4 B 508 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C23 PX4 A 509 " pdb=" O7 PX4 A 509 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 15095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18715 1.73 - 3.45: 1211 3.45 - 5.18: 268 5.18 - 6.91: 76 6.91 - 8.64: 45 Bond angle restraints: 20315 Sorted by residual: angle pdb=" CA PHE B 145 " pdb=" C PHE B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 120.77 127.90 -7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" CA PHE C 145 " pdb=" C PHE C 145 " pdb=" N PRO C 146 " ideal model delta sigma weight residual 120.77 127.90 -7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" CA PHE D 145 " pdb=" C PHE D 145 " pdb=" N PRO D 146 " ideal model delta sigma weight residual 120.77 127.90 -7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" CA PHE A 145 " pdb=" C PHE A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 120.77 127.88 -7.11 9.70e-01 1.06e+00 5.37e+01 angle pdb=" CA PHE E 145 " pdb=" C PHE E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 120.77 127.88 -7.11 9.70e-01 1.06e+00 5.37e+01 ... (remaining 20310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8025 17.24 - 34.48: 785 34.48 - 51.72: 295 51.72 - 68.96: 60 68.96 - 86.19: 15 Dihedral angle restraints: 9180 sinusoidal: 4045 harmonic: 5135 Sorted by residual: dihedral pdb=" CA TYR D 418 " pdb=" C TYR D 418 " pdb=" N LYS D 419 " pdb=" CA LYS D 419 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" CA TYR B 418 " pdb=" C TYR B 418 " pdb=" N LYS B 419 " pdb=" CA LYS B 419 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.48e+00 dihedral pdb=" N GLN B 171 " pdb=" CA GLN B 171 " pdb=" CB GLN B 171 " pdb=" CG GLN B 171 " ideal model delta sinusoidal sigma weight residual -180.00 -121.06 -58.94 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1817 0.063 - 0.126: 311 0.126 - 0.190: 67 0.190 - 0.253: 30 0.253 - 0.316: 20 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA ILE D 426 " pdb=" N ILE D 426 " pdb=" C ILE D 426 " pdb=" CB ILE D 426 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE C 426 " pdb=" N ILE C 426 " pdb=" C ILE C 426 " pdb=" CB ILE C 426 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ILE A 426 " pdb=" N ILE A 426 " pdb=" C ILE A 426 " pdb=" CB ILE A 426 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2242 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 224 " -0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LEU B 224 " 0.092 2.00e-02 2.50e+03 pdb=" O LEU B 224 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE B 225 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 224 " -0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LEU D 224 " 0.092 2.00e-02 2.50e+03 pdb=" O LEU D 224 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE D 225 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 224 " 0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C LEU A 224 " -0.092 2.00e-02 2.50e+03 pdb=" O LEU A 224 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE A 225 " 0.031 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 190 2.65 - 3.21: 12300 3.21 - 3.77: 22133 3.77 - 4.34: 32815 4.34 - 4.90: 52923 Nonbonded interactions: 120361 Sorted by model distance: nonbonded pdb=" OE2 GLU B 192 " pdb="ZN ZN B 502 " model vdw 2.083 2.230 nonbonded pdb=" OE2 GLU A 192 " pdb="ZN ZN A 502 " model vdw 2.083 2.230 nonbonded pdb=" OE2 GLU C 192 " pdb="ZN ZN C 502 " model vdw 2.083 2.230 nonbonded pdb=" OE2 GLU D 192 " pdb="ZN ZN D 502 " model vdw 2.083 2.230 nonbonded pdb=" OE2 GLU E 192 " pdb="ZN ZN E 601 " model vdw 2.083 2.230 ... (remaining 120356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 427 or resid 502 or (resid 508 and (name C1A or \ name C2A or name C3A or name C4A or name C5A or name C6A or name O1A or name O2C \ )))) selection = (chain 'B' and (resid 8 through 427 or resid 502 or (resid 507 and (name C1A or \ name C2A or name C3A or name C4A or name C5A or name C6A or name O1A or name O2C \ )))) selection = (chain 'C' and (resid 8 through 427 or resid 502 or (resid 507 and (name C1A or \ name C2A or name C3A or name C4A or name C5A or name C6A or name O1A or name O2C \ )))) selection = (chain 'D' and (resid 8 through 427 or resid 502 or (resid 507 and (name C1A or \ name C2A or name C3A or name C4A or name C5A or name C6A or name O1A or name O2C \ )))) selection = (chain 'E' and (resid 8 through 427 or resid 602 or resid 606)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.018 0.623 15130 Z= 0.812 Angle : 1.140 26.812 20355 Z= 0.685 Chirality : 0.062 0.316 2245 Planarity : 0.007 0.053 2520 Dihedral : 16.403 86.194 5825 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.96 % Allowed : 20.06 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1710 helix: -1.95 (0.16), residues: 565 sheet: -0.61 (0.25), residues: 405 loop : -1.12 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.013 0.001 TYR B 301 PHE 0.013 0.001 PHE D 13 TRP 0.024 0.003 TRP B 170 HIS 0.003 0.001 HIS E 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.56 (15100) covalent geometry : angle 1.04639 / 0.65 (20315) SS BOND : bond 0.48143 / 26.83 ( 5) SS BOND : angle 20.46356 / 10.45 ( 10) hydrogen bonds : bond 0.17426 / 11.55 ( 675) hydrogen bonds : angle 7.56967 / 5.12 ( 2250) metal coordination : bond 0.37178 / 25.12 ( 15) link_BETA1-4 : bond 0.00358 / 0.19 ( 5) link_BETA1-4 : angle 0.89143 / 0.50 ( 15) link_NAG-ASN : bond 0.00045 / 0.03 ( 5) link_NAG-ASN : angle 0.63786 / 0.34 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.442 Fit side-chains REVERT: A 171 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7934 (tm-30) REVERT: A 219 GLN cc_start: 0.8458 (mt0) cc_final: 0.8090 (mt0) REVERT: C 284 ASP cc_start: 0.8557 (m-30) cc_final: 0.8324 (m-30) REVERT: D 78 TYR cc_start: 0.8601 (t80) cc_final: 0.8315 (t80) REVERT: D 171 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7589 (tm-30) outliers start: 15 outliers final: 9 residues processed: 185 average time/residue: 0.4727 time to fit residues: 97.6210 Evaluate side-chains 145 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0070 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 226 GLN B 115 ASN C 115 ASN D 115 ASN E 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082699 restraints weight = 21198.024| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.22 r_work: 0.2961 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15130 Z= 0.149 Angle : 0.607 8.046 20355 Z= 0.308 Chirality : 0.043 0.142 2245 Planarity : 0.004 0.032 2520 Dihedral : 9.629 57.618 2438 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.18 % Allowed : 19.94 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 1710 helix: 0.63 (0.19), residues: 565 sheet: -0.03 (0.26), residues: 390 loop : -1.09 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 391 TYR 0.021 0.001 TYR A 301 PHE 0.011 0.001 PHE B 99 TRP 0.010 0.001 TRP A 170 HIS 0.003 0.001 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15100) covalent geometry : angle 0.60571 / 0.31 (20315) SS BOND : bond 0.00065 / 0.04 ( 5) SS BOND : angle 1.37753 / 0.71 ( 10) hydrogen bonds : bond 0.04855 / 3.17 ( 675) hydrogen bonds : angle 5.15378 / 3.53 ( 2250) metal coordination : bond 0.00468 / 0.27 ( 15) link_BETA1-4 : bond 0.00236 / 0.14 ( 5) link_BETA1-4 : angle 1.24337 / 0.71 ( 15) link_NAG-ASN : bond 0.00042 / 0.02 ( 5) link_NAG-ASN : angle 0.59788 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.617 Fit side-chains REVERT: A 171 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8433 (tm-30) REVERT: B 426 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7718 (tp) REVERT: C 78 TYR cc_start: 0.8862 (t80) cc_final: 0.8633 (t80) REVERT: C 80 ASP cc_start: 0.7463 (t0) cc_final: 0.7204 (t0) REVERT: C 89 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7500 (pp-130) REVERT: D 171 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8241 (tm-30) outliers start: 50 outliers final: 9 residues processed: 193 average time/residue: 0.5021 time to fit residues: 108.4920 Evaluate side-chains 147 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 121 optimal weight: 0.0070 chunk 14 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 HIS B 42 ASN B 201 HIS C 201 HIS D 42 ASN D 115 ASN D 201 HIS E 42 ASN E 201 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084831 restraints weight = 21579.271| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.25 r_work: 0.3004 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15130 Z= 0.103 Angle : 0.521 5.830 20355 Z= 0.267 Chirality : 0.041 0.143 2245 Planarity : 0.003 0.027 2520 Dihedral : 8.951 80.578 2427 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.61 % Allowed : 19.62 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1710 helix: 1.29 (0.21), residues: 595 sheet: 0.22 (0.28), residues: 390 loop : -0.74 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 309 TYR 0.020 0.001 TYR D 301 PHE 0.012 0.001 PHE B 121 TRP 0.008 0.001 TRP A 239 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15100) covalent geometry : angle 0.52021 / 0.27 (20315) SS BOND : bond 0.00135 / 0.07 ( 5) SS BOND : angle 1.07487 / 0.55 ( 10) hydrogen bonds : bond 0.03959 / 2.58 ( 675) hydrogen bonds : angle 4.56707 / 3.11 ( 2250) metal coordination : bond 0.00219 / 0.14 ( 15) link_BETA1-4 : bond 0.00297 / 0.18 ( 5) link_BETA1-4 : angle 1.07351 / 0.62 ( 15) link_NAG-ASN : bond 0.00157 / 0.09 ( 5) link_NAG-ASN : angle 0.39799 / 0.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.589 Fit side-chains REVERT: A 132 LEU cc_start: 0.9088 (mt) cc_final: 0.8886 (mt) REVERT: A 171 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8174 (mm-40) REVERT: A 173 GLU cc_start: 0.8164 (pm20) cc_final: 0.7950 (pm20) REVERT: A 255 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8198 (tt) REVERT: E 309 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7498 (ptt90) outliers start: 41 outliers final: 8 residues processed: 183 average time/residue: 0.5000 time to fit residues: 102.2736 Evaluate side-chains 147 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078472 restraints weight = 21801.357| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.25 r_work: 0.2886 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15130 Z= 0.259 Angle : 0.651 6.909 20355 Z= 0.334 Chirality : 0.046 0.178 2245 Planarity : 0.004 0.057 2520 Dihedral : 9.228 58.640 2425 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.95 % Allowed : 19.30 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1710 helix: 1.42 (0.21), residues: 600 sheet: 0.06 (0.27), residues: 395 loop : -0.94 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 29 TYR 0.025 0.002 TYR A 301 PHE 0.014 0.002 PHE A 48 TRP 0.014 0.002 TRP A 170 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (15100) covalent geometry : angle 0.64851 / 0.33 (20315) SS BOND : bond 0.00492 / 0.28 ( 5) SS BOND : angle 1.76667 / 0.91 ( 10) hydrogen bonds : bond 0.05109 / 3.30 ( 675) hydrogen bonds : angle 4.93916 / 3.38 ( 2250) metal coordination : bond 0.00712 / 0.46 ( 15) link_BETA1-4 : bond 0.00177 / 0.11 ( 5) link_BETA1-4 : angle 1.49104 / 0.89 ( 15) link_NAG-ASN : bond 0.00345 / 0.19 ( 5) link_NAG-ASN : angle 1.06454 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 0.498 Fit side-chains REVERT: A 171 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 173 GLU cc_start: 0.8316 (pm20) cc_final: 0.8108 (pm20) REVERT: A 233 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8932 (mp) REVERT: A 255 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 309 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7596 (ptt-90) REVERT: A 393 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8040 (mtpt) REVERT: B 191 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: B 255 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8196 (tt) REVERT: B 393 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: C 247 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8408 (p0) REVERT: C 255 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 309 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7325 (ptt-90) REVERT: C 393 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (mtpp) REVERT: D 191 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: D 393 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8214 (mtpt) REVERT: E 309 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7565 (ptt90) REVERT: E 393 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8038 (mtpp) outliers start: 62 outliers final: 21 residues processed: 186 average time/residue: 0.5565 time to fit residues: 113.9139 Evaluate side-chains 171 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN E 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081483 restraints weight = 21913.670| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.29 r_work: 0.2942 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15130 Z= 0.123 Angle : 0.541 7.249 20355 Z= 0.277 Chirality : 0.043 0.176 2245 Planarity : 0.003 0.033 2520 Dihedral : 8.523 59.816 2425 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.12 % Allowed : 20.51 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1710 helix: 1.89 (0.21), residues: 565 sheet: 0.21 (0.27), residues: 390 loop : -0.82 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 252 TYR 0.021 0.001 TYR A 301 PHE 0.011 0.001 PHE A 99 TRP 0.008 0.001 TRP C 170 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15100) covalent geometry : angle 0.54058 / 0.28 (20315) SS BOND : bond 0.00221 / 0.12 ( 5) SS BOND : angle 0.89059 / 0.46 ( 10) hydrogen bonds : bond 0.04084 / 2.66 ( 675) hydrogen bonds : angle 4.47772 / 3.06 ( 2250) metal coordination : bond 0.00297 / 0.19 ( 15) link_BETA1-4 : bond 0.00356 / 0.20 ( 5) link_BETA1-4 : angle 1.06579 / 0.62 ( 15) link_NAG-ASN : bond 0.00097 / 0.06 ( 5) link_NAG-ASN : angle 0.60046 / 0.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.590 Fit side-chains REVERT: A 89 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7509 (ppp) REVERT: A 171 GLN cc_start: 0.8791 (mm-40) cc_final: 0.7815 (mm-40) REVERT: A 173 GLU cc_start: 0.8327 (pm20) cc_final: 0.7908 (pm20) REVERT: A 177 GLN cc_start: 0.8894 (mt0) cc_final: 0.8480 (mt0) REVERT: A 255 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 309 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7531 (ptt-90) REVERT: A 393 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8008 (mtpt) REVERT: B 255 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 393 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8186 (mtpp) REVERT: C 173 GLU cc_start: 0.8489 (pm20) cc_final: 0.8148 (pm20) REVERT: C 309 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7387 (ptt-90) REVERT: C 393 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: D 191 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: D 393 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8206 (mtpt) REVERT: E 309 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7561 (ptt90) REVERT: E 393 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8016 (mtpp) outliers start: 49 outliers final: 13 residues processed: 187 average time/residue: 0.5587 time to fit residues: 115.1100 Evaluate side-chains 165 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082087 restraints weight = 21808.503| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.27 r_work: 0.2948 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15130 Z= 0.122 Angle : 0.541 8.462 20355 Z= 0.275 Chirality : 0.043 0.184 2245 Planarity : 0.003 0.032 2520 Dihedral : 8.160 58.053 2425 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.06 % Allowed : 21.53 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1710 helix: 1.99 (0.21), residues: 565 sheet: 0.29 (0.28), residues: 390 loop : -0.80 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.022 0.001 TYR A 301 PHE 0.013 0.001 PHE E 121 TRP 0.009 0.001 TRP B 170 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15100) covalent geometry : angle 0.53943 / 0.28 (20315) SS BOND : bond 0.00268 / 0.15 ( 5) SS BOND : angle 0.93633 / 0.48 ( 10) hydrogen bonds : bond 0.03997 / 2.60 ( 675) hydrogen bonds : angle 4.41035 / 3.01 ( 2250) metal coordination : bond 0.00287 / 0.18 ( 15) link_BETA1-4 : bond 0.00274 / 0.15 ( 5) link_BETA1-4 : angle 1.17044 / 0.69 ( 15) link_NAG-ASN : bond 0.00028 / 0.01 ( 5) link_NAG-ASN : angle 0.67084 / 0.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.644 Fit side-chains REVERT: A 89 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7538 (ppp) REVERT: A 171 GLN cc_start: 0.8763 (mm-40) cc_final: 0.7734 (tm-30) REVERT: A 173 GLU cc_start: 0.8347 (pm20) cc_final: 0.7900 (pm20) REVERT: A 255 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 309 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7504 (ptt-90) REVERT: A 393 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (mtpp) REVERT: B 255 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8218 (tt) REVERT: B 393 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: C 173 GLU cc_start: 0.8494 (pm20) cc_final: 0.8193 (pm20) REVERT: C 309 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7366 (ptt-90) REVERT: C 393 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (mtpp) REVERT: D 191 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: D 393 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8213 (mtpt) REVERT: D 426 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7713 (tp) REVERT: E 173 GLU cc_start: 0.8481 (pm20) cc_final: 0.8245 (pm20) REVERT: E 393 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8026 (mtpp) outliers start: 48 outliers final: 16 residues processed: 183 average time/residue: 0.5919 time to fit residues: 119.9458 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 146 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082044 restraints weight = 21795.808| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.27 r_work: 0.2958 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15130 Z= 0.133 Angle : 0.585 10.395 20355 Z= 0.294 Chirality : 0.043 0.190 2245 Planarity : 0.003 0.033 2520 Dihedral : 7.971 56.603 2425 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.06 % Allowed : 21.21 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1710 helix: 2.02 (0.21), residues: 565 sheet: 0.29 (0.28), residues: 390 loop : -0.77 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.022 0.001 TYR A 301 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP A 170 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (15100) covalent geometry : angle 0.57519 / 0.29 (20315) SS BOND : bond 0.01050 / 0.58 ( 5) SS BOND : angle 4.60264 / 2.37 ( 10) hydrogen bonds : bond 0.03963 / 2.58 ( 675) hydrogen bonds : angle 4.42446 / 3.03 ( 2250) metal coordination : bond 0.00306 / 0.19 ( 15) link_BETA1-4 : bond 0.00330 / 0.19 ( 5) link_BETA1-4 : angle 1.18857 / 0.69 ( 15) link_NAG-ASN : bond 0.00039 / 0.02 ( 5) link_NAG-ASN : angle 0.69390 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.609 Fit side-chains REVERT: A 89 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7541 (ppp) REVERT: A 171 GLN cc_start: 0.8766 (mm-40) cc_final: 0.7765 (mm-40) REVERT: A 173 GLU cc_start: 0.8369 (pm20) cc_final: 0.7956 (pm20) REVERT: A 233 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 255 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 309 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7480 (ptt-90) REVERT: A 393 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8041 (mtpp) REVERT: B 173 GLU cc_start: 0.8377 (pm20) cc_final: 0.8146 (pm20) REVERT: B 255 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 393 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8194 (mtpp) REVERT: C 173 GLU cc_start: 0.8478 (pm20) cc_final: 0.8176 (pm20) REVERT: C 309 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7380 (ptt-90) REVERT: C 393 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8155 (mtpp) REVERT: D 191 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: D 393 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: E 173 GLU cc_start: 0.8479 (pm20) cc_final: 0.8258 (pm20) REVERT: E 309 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7581 (ptt90) REVERT: E 393 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8002 (mtpp) outliers start: 48 outliers final: 14 residues processed: 181 average time/residue: 0.6320 time to fit residues: 125.9963 Evaluate side-chains 167 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 138 optimal weight: 0.0020 chunk 97 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.083704 restraints weight = 21912.532| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.27 r_work: 0.2977 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15130 Z= 0.108 Angle : 0.553 9.864 20355 Z= 0.278 Chirality : 0.042 0.189 2245 Planarity : 0.003 0.029 2520 Dihedral : 7.421 56.632 2425 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.23 % Allowed : 22.10 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1710 helix: 2.13 (0.21), residues: 565 sheet: 0.36 (0.28), residues: 390 loop : -0.74 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 252 TYR 0.020 0.001 TYR A 301 PHE 0.017 0.001 PHE E 121 TRP 0.008 0.001 TRP A 170 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15100) covalent geometry : angle 0.54437 / 0.27 (20315) SS BOND : bond 0.00522 / 0.29 ( 5) SS BOND : angle 4.22432 / 2.18 ( 10) hydrogen bonds : bond 0.03649 / 2.38 ( 675) hydrogen bonds : angle 4.27826 / 2.93 ( 2250) metal coordination : bond 0.00232 / 0.14 ( 15) link_BETA1-4 : bond 0.00285 / 0.16 ( 5) link_BETA1-4 : angle 1.11054 / 0.65 ( 15) link_NAG-ASN : bond 0.00054 / 0.03 ( 5) link_NAG-ASN : angle 0.59579 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.603 Fit side-chains REVERT: A 89 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7533 (ppp) REVERT: A 171 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8044 (mm-40) REVERT: A 173 GLU cc_start: 0.8369 (pm20) cc_final: 0.8051 (pm20) REVERT: A 255 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8294 (tt) REVERT: A 309 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7438 (ptt-90) REVERT: A 393 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8007 (mtpp) REVERT: B 173 GLU cc_start: 0.8356 (pm20) cc_final: 0.8137 (pm20) REVERT: B 255 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8215 (tt) REVERT: B 393 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: C 173 GLU cc_start: 0.8499 (pm20) cc_final: 0.8232 (pm20) REVERT: C 393 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (mmmm) REVERT: D 191 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: D 393 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: E 393 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8034 (mtpp) outliers start: 35 outliers final: 13 residues processed: 181 average time/residue: 0.6073 time to fit residues: 121.3381 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 149 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083412 restraints weight = 21919.720| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.28 r_work: 0.2974 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15130 Z= 0.117 Angle : 0.568 11.191 20355 Z= 0.285 Chirality : 0.042 0.196 2245 Planarity : 0.003 0.031 2520 Dihedral : 7.304 57.161 2425 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.91 % Allowed : 22.42 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1710 helix: 2.12 (0.21), residues: 565 sheet: 0.33 (0.27), residues: 395 loop : -0.75 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.021 0.001 TYR A 301 PHE 0.017 0.001 PHE D 121 TRP 0.009 0.001 TRP E 170 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15100) covalent geometry : angle 0.56055 / 0.28 (20315) SS BOND : bond 0.00344 / 0.19 ( 5) SS BOND : angle 3.96798 / 2.05 ( 10) hydrogen bonds : bond 0.03677 / 2.40 ( 675) hydrogen bonds : angle 4.27559 / 2.93 ( 2250) metal coordination : bond 0.00259 / 0.16 ( 15) link_BETA1-4 : bond 0.00293 / 0.17 ( 5) link_BETA1-4 : angle 1.15747 / 0.68 ( 15) link_NAG-ASN : bond 0.00034 / 0.02 ( 5) link_NAG-ASN : angle 0.62914 / 0.34 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.595 Fit side-chains REVERT: A 80 ASP cc_start: 0.7976 (m-30) cc_final: 0.7661 (m-30) REVERT: A 89 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7532 (ppp) REVERT: A 171 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8069 (mm-40) REVERT: A 173 GLU cc_start: 0.8374 (pm20) cc_final: 0.8064 (pm20) REVERT: A 233 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8917 (mp) REVERT: A 255 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 309 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7443 (ptt-90) REVERT: A 393 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8027 (mmmm) REVERT: B 173 GLU cc_start: 0.8354 (pm20) cc_final: 0.8133 (pm20) REVERT: B 255 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 393 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: C 173 GLU cc_start: 0.8469 (pm20) cc_final: 0.8204 (pm20) REVERT: C 393 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8105 (mmmm) REVERT: D 191 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: D 393 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: E 393 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (mtpp) outliers start: 30 outliers final: 16 residues processed: 173 average time/residue: 0.6165 time to fit residues: 117.8015 Evaluate side-chains 173 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082802 restraints weight = 21817.106| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.27 r_work: 0.2960 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15130 Z= 0.125 Angle : 0.570 11.610 20355 Z= 0.287 Chirality : 0.043 0.202 2245 Planarity : 0.003 0.030 2520 Dihedral : 7.225 58.370 2425 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.97 % Allowed : 22.42 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1710 helix: 2.12 (0.21), residues: 565 sheet: 0.34 (0.27), residues: 395 loop : -0.73 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.022 0.001 TYR A 301 PHE 0.019 0.001 PHE E 121 TRP 0.010 0.001 TRP E 170 HIS 0.001 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (15100) covalent geometry : angle 0.56331 / 0.28 (20315) SS BOND : bond 0.00325 / 0.18 ( 5) SS BOND : angle 3.88166 / 2.00 ( 10) hydrogen bonds : bond 0.03754 / 2.45 ( 675) hydrogen bonds : angle 4.29577 / 2.94 ( 2250) metal coordination : bond 0.00280 / 0.18 ( 15) link_BETA1-4 : bond 0.00238 / 0.13 ( 5) link_BETA1-4 : angle 1.17361 / 0.69 ( 15) link_NAG-ASN : bond 0.00028 / 0.01 ( 5) link_NAG-ASN : angle 0.68890 / 0.37 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.612 Fit side-chains REVERT: A 89 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (ppp) REVERT: A 171 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8082 (mm-40) REVERT: A 173 GLU cc_start: 0.8394 (pm20) cc_final: 0.8084 (pm20) REVERT: A 233 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8915 (mp) REVERT: A 255 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 309 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7441 (ptt-90) REVERT: A 393 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8034 (mmmm) REVERT: B 173 GLU cc_start: 0.8367 (pm20) cc_final: 0.8154 (pm20) REVERT: B 255 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 393 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8188 (mmmm) REVERT: C 173 GLU cc_start: 0.8472 (pm20) cc_final: 0.8210 (pm20) REVERT: C 393 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8105 (mmmm) REVERT: D 80 ASP cc_start: 0.7277 (t0) cc_final: 0.7075 (t0) REVERT: D 191 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 393 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: E 393 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8061 (mtpp) outliers start: 31 outliers final: 16 residues processed: 172 average time/residue: 0.6146 time to fit residues: 116.9154 Evaluate side-chains 173 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083391 restraints weight = 21785.881| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.28 r_work: 0.2971 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15130 Z= 0.115 Angle : 0.571 10.043 20355 Z= 0.286 Chirality : 0.043 0.199 2245 Planarity : 0.003 0.039 2520 Dihedral : 7.105 58.896 2425 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.85 % Allowed : 22.68 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1710 helix: 2.15 (0.22), residues: 565 sheet: 0.34 (0.27), residues: 395 loop : -0.70 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 309 TYR 0.021 0.001 TYR A 301 PHE 0.019 0.001 PHE B 121 TRP 0.009 0.001 TRP E 170 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (15100) covalent geometry : angle 0.56449 / 0.28 (20315) SS BOND : bond 0.00328 / 0.18 ( 5) SS BOND : angle 3.78432 / 1.95 ( 10) hydrogen bonds : bond 0.03661 / 2.39 ( 675) hydrogen bonds : angle 4.23244 / 2.90 ( 2250) metal coordination : bond 0.00244 / 0.15 ( 15) link_BETA1-4 : bond 0.00274 / 0.15 ( 5) link_BETA1-4 : angle 1.13949 / 0.66 ( 15) link_NAG-ASN : bond 0.00033 / 0.02 ( 5) link_NAG-ASN : angle 0.63638 / 0.35 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.34 seconds wall clock time: 101 minutes 58.60 seconds (6118.60 seconds total)