Starting phenix.real_space_refine on Fri Sep 27 15:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/09_2024/6uzy_20964.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 10948 2.51 5 N 2443 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16212 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "D" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "E" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "F" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "G" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.87, per 1000 atoms: 0.61 Number of scatterers: 16212 At special positions: 0 Unit cell: (107.8, 107.8, 123.2, 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) S 77 16.00 P 7 15.00 O 2737 8.00 N 2443 7.00 C 10948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.1 seconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3794 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 71.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.612A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.894A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.612A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.896A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 240 removed outlier: 4.098A pdb=" N LYS C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.612A pdb=" N LEU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 286 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.611A pdb=" N LEU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.655A pdb=" N LYS E 205 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 240 removed outlier: 4.098A pdb=" N LYS E 214 " --> pdb=" O GLY E 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 removed outlier: 3.590A pdb=" N ARG E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR E 286 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.612A pdb=" N LEU E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS F 205 " --> pdb=" O TYR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS F 214 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN F 282 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR F 286 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Proline residue: F 291 - end of helix removed outlier: 3.611A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 237 " --> pdb=" O LEU G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 286 " --> pdb=" O ASN G 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G 290 " --> pdb=" O TYR G 286 " (cutoff:3.500A) Proline residue: G 291 - end of helix removed outlier: 3.612A pdb=" N LEU G 298 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 966 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3216 1.46 - 1.58: 8863 1.58 - 1.70: 140 1.70 - 1.82: 112 Bond restraints: 16569 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU D 501 " pdb=" O18 6OU D 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU E 501 " pdb=" O18 6OU E 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 16564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 21997 3.23 - 6.46: 319 6.46 - 9.69: 70 9.69 - 12.92: 0 12.92 - 16.15: 7 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N HIS F 106 " pdb=" CA HIS F 106 " pdb=" C HIS F 106 " ideal model delta sigma weight residual 111.28 118.19 -6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N HIS D 106 " pdb=" CA HIS D 106 " pdb=" C HIS D 106 " ideal model delta sigma weight residual 111.28 118.17 -6.89 1.09e+00 8.42e-01 4.00e+01 angle pdb=" N HIS B 106 " pdb=" CA HIS B 106 " pdb=" C HIS B 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS A 106 " pdb=" CA HIS A 106 " pdb=" C HIS A 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS E 106 " pdb=" CA HIS E 106 " pdb=" C HIS E 106 " ideal model delta sigma weight residual 111.28 118.11 -6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 9576 32.10 - 64.21: 336 64.21 - 96.31: 21 96.31 - 128.41: 0 128.41 - 160.52: 21 Dihedral angle restraints: 9954 sinusoidal: 4123 harmonic: 5831 Sorted by residual: dihedral pdb=" C ASN B 306 " pdb=" N ASN B 306 " pdb=" CA ASN B 306 " pdb=" CB ASN B 306 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C ASN F 306 " pdb=" N ASN F 306 " pdb=" CA ASN F 306 " pdb=" CB ASN F 306 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C ASN G 306 " pdb=" N ASN G 306 " pdb=" CA ASN G 306 " pdb=" CB ASN G 306 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 9951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2457 0.112 - 0.225: 169 0.225 - 0.337: 6 0.337 - 0.450: 0 0.450 - 0.562: 14 Chirality restraints: 2646 Sorted by residual: chirality pdb=" C20 6OU G1002 " pdb=" C19 6OU G1002 " pdb=" C21 6OU G1002 " pdb=" O30 6OU G1002 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C20 6OU C 501 " pdb=" C19 6OU C 501 " pdb=" C21 6OU C 501 " pdb=" O30 6OU C 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" C20 6OU F 501 " pdb=" C19 6OU F 501 " pdb=" C21 6OU F 501 " pdb=" O30 6OU F 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 2643 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 290 " -0.032 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 291 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 290 " 0.032 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO E 291 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 291 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 291 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.032 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO E 133 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.027 5.00e-02 4.00e+02 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3924 2.79 - 3.32: 14483 3.32 - 3.85: 24815 3.85 - 4.37: 29118 4.37 - 4.90: 52268 Nonbonded interactions: 124608 Sorted by model distance: nonbonded pdb=" NH2 ARG B 75 " pdb=" OD2 ASP C 81 " model vdw 2.265 3.120 nonbonded pdb=" NE2 GLN C 76 " pdb=" O ALA D 68 " model vdw 2.345 3.120 nonbonded pdb=" OH TYR G 311 " pdb=" OG SER G 346 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR F 311 " pdb=" OG SER F 346 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR B 311 " pdb=" OG SER B 346 " model vdw 2.361 3.040 ... (remaining 124603 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 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'B' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'C' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'D' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'E' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'F' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'G' and (resid 25 through 358 or resid 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.950 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.012 0.136 16569 Z= 0.737 Angle : 1.097 16.145 22393 Z= 0.617 Chirality : 0.073 0.562 2646 Planarity : 0.006 0.047 2625 Dihedral : 17.598 160.518 6118 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.16), residues: 1890 helix: -1.77 (0.12), residues: 1407 sheet: -0.71 (0.54), residues: 77 loop : -3.77 (0.23), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 74 HIS 0.003 0.001 HIS G 330 PHE 0.013 0.001 PHE G 246 TYR 0.010 0.001 TYR G 280 ARG 0.003 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.699 Fit side-chains REVERT: B 52 LEU cc_start: 0.7829 (mt) cc_final: 0.7546 (mt) REVERT: B 128 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8006 (ttp80) REVERT: D 235 TYR cc_start: 0.7276 (t80) cc_final: 0.7036 (t80) REVERT: D 282 ASN cc_start: 0.8530 (t0) cc_final: 0.8330 (t0) REVERT: E 297 MET cc_start: 0.8656 (mtp) cc_final: 0.8428 (mtm) REVERT: F 52 LEU cc_start: 0.8004 (mt) cc_final: 0.7770 (mt) REVERT: F 235 TYR cc_start: 0.7253 (t80) cc_final: 0.7046 (t80) REVERT: G 290 MET cc_start: 0.7909 (mtp) cc_final: 0.7588 (mtt) REVERT: G 309 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7704 (mtpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3016 time to fit residues: 67.0451 Evaluate side-chains 116 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16569 Z= 0.167 Angle : 0.533 5.871 22393 Z= 0.269 Chirality : 0.038 0.127 2646 Planarity : 0.004 0.031 2625 Dihedral : 11.048 107.477 2415 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.45 % Allowed : 11.90 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1890 helix: 0.26 (0.14), residues: 1435 sheet: -2.40 (0.45), residues: 119 loop : -3.01 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.002 0.001 HIS G 330 PHE 0.006 0.001 PHE C 349 TYR 0.007 0.001 TYR E 215 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.842 Fit side-chains REVERT: B 290 MET cc_start: 0.7348 (mtp) cc_final: 0.7111 (mtt) REVERT: D 203 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8141 (mtpt) REVERT: E 203 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8195 (mtpt) REVERT: F 52 LEU cc_start: 0.8042 (mt) cc_final: 0.7783 (mt) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.2452 time to fit residues: 49.4070 Evaluate side-chains 108 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16569 Z= 0.160 Angle : 0.503 5.700 22393 Z= 0.251 Chirality : 0.037 0.122 2646 Planarity : 0.003 0.028 2625 Dihedral : 9.367 104.545 2415 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.85 % Allowed : 14.80 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1890 helix: 1.01 (0.14), residues: 1435 sheet: -2.48 (0.61), residues: 84 loop : -2.56 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 74 HIS 0.002 0.001 HIS C 330 PHE 0.006 0.001 PHE A 126 TYR 0.007 0.001 TYR F 215 ARG 0.001 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5864 (mtt180) REVERT: B 290 MET cc_start: 0.7375 (mtp) cc_final: 0.7169 (mtt) REVERT: E 244 ASP cc_start: 0.7243 (p0) cc_final: 0.6869 (p0) REVERT: F 52 LEU cc_start: 0.8001 (mt) cc_final: 0.7663 (mt) REVERT: F 282 ASN cc_start: 0.8383 (t0) cc_final: 0.7985 (m-40) REVERT: G 29 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6107 (mtt180) REVERT: G 282 ASN cc_start: 0.8368 (t0) cc_final: 0.8063 (t0) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 0.2559 time to fit residues: 50.7730 Evaluate side-chains 112 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN G 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16569 Z= 0.178 Angle : 0.502 5.623 22393 Z= 0.250 Chirality : 0.038 0.122 2646 Planarity : 0.003 0.028 2625 Dihedral : 9.198 108.664 2415 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.76 % Allowed : 15.53 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1890 helix: 1.38 (0.14), residues: 1435 sheet: -2.07 (0.49), residues: 119 loop : -2.57 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS G 330 PHE 0.007 0.001 PHE B 333 TYR 0.008 0.001 TYR F 215 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6049 (mtt180) REVERT: B 290 MET cc_start: 0.7387 (mtp) cc_final: 0.7167 (mtt) REVERT: E 244 ASP cc_start: 0.7241 (p0) cc_final: 0.6836 (p0) REVERT: G 29 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6135 (mtt180) REVERT: G 309 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7992 (mtpp) outliers start: 31 outliers final: 18 residues processed: 118 average time/residue: 0.2799 time to fit residues: 50.6969 Evaluate side-chains 117 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 7.9990 chunk 103 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16569 Z= 0.195 Angle : 0.509 5.606 22393 Z= 0.253 Chirality : 0.038 0.122 2646 Planarity : 0.003 0.060 2625 Dihedral : 9.221 111.542 2415 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.59 % Allowed : 16.33 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1890 helix: 1.53 (0.14), residues: 1435 sheet: -2.44 (0.62), residues: 84 loop : -2.18 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.002 0.001 HIS E 330 PHE 0.007 0.001 PHE B 333 TYR 0.008 0.001 TYR A 215 ARG 0.005 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6668 (mtt90) REVERT: B 29 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6106 (mtt180) REVERT: B 290 MET cc_start: 0.7422 (mtp) cc_final: 0.7165 (mtt) REVERT: E 244 ASP cc_start: 0.7167 (p0) cc_final: 0.6770 (p0) REVERT: G 29 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6207 (mtt180) REVERT: G 31 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7089 (mt-10) outliers start: 28 outliers final: 23 residues processed: 121 average time/residue: 0.2704 time to fit residues: 51.0813 Evaluate side-chains 124 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.144 Angle : 0.475 5.540 22393 Z= 0.236 Chirality : 0.037 0.120 2646 Planarity : 0.003 0.040 2625 Dihedral : 8.969 110.435 2415 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.91 % Allowed : 18.08 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1890 helix: 1.79 (0.15), residues: 1435 sheet: -2.44 (0.62), residues: 84 loop : -2.07 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 PHE 0.006 0.001 PHE C 126 TYR 0.007 0.001 TYR A 215 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6604 (mtt180) REVERT: B 290 MET cc_start: 0.7364 (mtp) cc_final: 0.7154 (mtt) REVERT: D 28 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8033 (mp) REVERT: E 244 ASP cc_start: 0.7079 (p0) cc_final: 0.6677 (p0) REVERT: G 31 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7067 (mt-10) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.2622 time to fit residues: 47.3523 Evaluate side-chains 116 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN B 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16569 Z= 0.160 Angle : 0.483 5.562 22393 Z= 0.239 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.045 2625 Dihedral : 8.968 111.694 2415 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.30 % Allowed : 18.25 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1890 helix: 1.87 (0.15), residues: 1435 sheet: -2.49 (0.62), residues: 84 loop : -1.95 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 PHE 0.007 0.001 PHE B 333 TYR 0.007 0.001 TYR A 215 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6005 (mtt180) REVERT: B 128 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7894 (ttm170) REVERT: B 290 MET cc_start: 0.7388 (mtp) cc_final: 0.7153 (mtt) REVERT: D 28 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 244 ASP cc_start: 0.7074 (p0) cc_final: 0.6661 (p0) REVERT: G 28 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (mp) REVERT: G 29 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6268 (mtt180) REVERT: G 31 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7102 (mt-10) outliers start: 23 outliers final: 19 residues processed: 122 average time/residue: 0.2796 time to fit residues: 52.6773 Evaluate side-chains 125 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16569 Z= 0.202 Angle : 0.509 5.605 22393 Z= 0.252 Chirality : 0.038 0.122 2646 Planarity : 0.003 0.051 2625 Dihedral : 9.186 114.561 2415 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 18.88 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1890 helix: 1.82 (0.15), residues: 1435 sheet: -2.09 (0.49), residues: 119 loop : -2.06 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.002 0.001 HIS E 330 PHE 0.008 0.001 PHE B 333 TYR 0.008 0.001 TYR A 215 ARG 0.005 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6160 (mtt180) REVERT: B 290 MET cc_start: 0.7423 (mtp) cc_final: 0.7154 (mtt) REVERT: D 28 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8183 (mp) REVERT: D 290 MET cc_start: 0.7275 (mtt) cc_final: 0.6975 (mtt) REVERT: E 28 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8027 (mp) REVERT: E 244 ASP cc_start: 0.7146 (p0) cc_final: 0.6728 (p0) REVERT: G 28 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8226 (mp) REVERT: G 29 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6366 (mtt180) REVERT: G 31 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7072 (mt-10) outliers start: 28 outliers final: 21 residues processed: 122 average time/residue: 0.2867 time to fit residues: 53.5701 Evaluate side-chains 129 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 169 optimal weight: 0.6980 chunk 102 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN D 106 HIS F 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.130 Angle : 0.461 5.508 22393 Z= 0.228 Chirality : 0.036 0.120 2646 Planarity : 0.003 0.040 2625 Dihedral : 8.821 112.075 2415 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.13 % Allowed : 19.27 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1890 helix: 2.04 (0.15), residues: 1435 sheet: -2.52 (0.60), residues: 84 loop : -1.81 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS G 106 PHE 0.005 0.001 PHE C 126 TYR 0.007 0.000 TYR A 215 ARG 0.001 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6549 (mtt180) REVERT: B 29 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.5986 (mtt180) REVERT: B 128 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7939 (ttm170) REVERT: D 239 LEU cc_start: 0.8275 (tp) cc_final: 0.8045 (tp) REVERT: E 28 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7838 (mp) REVERT: E 244 ASP cc_start: 0.7037 (p0) cc_final: 0.6625 (p0) REVERT: F 29 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6279 (mtt180) REVERT: G 28 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8114 (mp) REVERT: G 29 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6228 (mtt180) REVERT: G 31 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7022 (mt-10) outliers start: 20 outliers final: 12 residues processed: 129 average time/residue: 0.3002 time to fit residues: 58.8634 Evaluate side-chains 123 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 29 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 159 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN E 106 HIS G 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.135 Angle : 0.467 5.525 22393 Z= 0.231 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.039 2625 Dihedral : 8.780 112.419 2415 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.08 % Allowed : 19.67 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1890 helix: 2.14 (0.15), residues: 1428 sheet: -2.52 (0.60), residues: 84 loop : -1.89 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS G 330 PHE 0.007 0.001 PHE C 126 TYR 0.006 0.000 TYR F 215 ARG 0.002 0.000 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.5905 (mtt180) REVERT: B 128 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7936 (ttm170) REVERT: D 239 LEU cc_start: 0.8285 (tp) cc_final: 0.8082 (tp) REVERT: E 244 ASP cc_start: 0.7091 (p0) cc_final: 0.6640 (p0) REVERT: F 29 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6300 (mtt180) REVERT: G 28 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (mp) REVERT: G 29 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6104 (mtt180) REVERT: G 31 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7033 (mt-10) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.2867 time to fit residues: 51.1181 Evaluate side-chains 116 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109738 restraints weight = 16622.773| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.69 r_work: 0.3009 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16569 Z= 0.151 Angle : 0.474 5.548 22393 Z= 0.235 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.040 2625 Dihedral : 8.823 113.516 2415 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.96 % Allowed : 19.73 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.21), residues: 1890 helix: 2.13 (0.15), residues: 1428 sheet: -2.50 (0.59), residues: 84 loop : -1.91 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS E 330 PHE 0.006 0.001 PHE C 126 TYR 0.007 0.001 TYR F 215 ARG 0.003 0.000 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.26 seconds wall clock time: 49 minutes 24.41 seconds (2964.41 seconds total)