Starting phenix.real_space_refine on Fri Jul 3 18:57:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egs_47996/07_2026/9egs_47996.map" } resolution = 2.45 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= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 85 5.16 5 Cl 10 4.86 5 C 10230 2.51 5 N 2540 2.21 5 O 2935 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: 15805 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3182 Chain: "B" Number of atoms: 3104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3182 Chain: "C" Number of atoms: 3104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3182 Chain: "D" Number of atoms: 3104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3182 Chain: "E" Number of atoms: 3104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 377, 3096 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3182 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 2} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 2} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 2} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AMET A 214 " occ=0.36 ... (14 atoms not shown) pdb=" CE BMET A 214 " occ=0.64 residue: pdb=" N AMET B 214 " occ=0.36 ... (14 atoms not shown) pdb=" CE BMET B 214 " occ=0.64 residue: pdb=" N AMET C 214 " occ=0.36 ... (14 atoms not shown) pdb=" CE BMET C 214 " occ=0.64 residue: pdb=" N AMET D 214 " occ=0.36 ... (14 atoms not shown) pdb=" CE BMET D 214 " occ=0.64 residue: pdb=" N AMET E 214 " occ=0.36 ... (14 atoms not shown) pdb=" CE BMET E 214 " occ=0.64 Time building chain proxies: 6.50, per 1000 atoms: 0.41 Number of scatterers: 15805 At special positions: 0 Unit cell: (107.3, 105.85, 109.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 85 16.00 O 2935 8.00 N 2540 7.00 C 10230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 1.3 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: 3610 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 5 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.580A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.704A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.783A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.545A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.562A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.612A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.516A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.868A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.721A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.537A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.579A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.704A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.783A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 3.545A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.562A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.612A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.517A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.869A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.720A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.538A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.579A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.703A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.783A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.545A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.562A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.613A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.517A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.869A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.722A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.537A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.579A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.702A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.783A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.545A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.562A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.612A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.516A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.868A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.721A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.537A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.579A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.704A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.784A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.544A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.561A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.613A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.516A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.869A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.721A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.538A pdb=" N GLU E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.495A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.497A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.493A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 376 removed outlier: 4.494A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.494A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2840 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: 2.72 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4799 1.34 - 1.46: 3791 1.46 - 1.58: 7265 1.58 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 16000 Sorted by residual: bond pdb=" C LYS B 340 " pdb=" O LYS B 340 " ideal model delta sigma weight residual 1.244 1.237 0.007 9.30e-03 1.16e+04 5.09e-01 bond pdb=" C LYS A 340 " pdb=" O LYS A 340 " ideal model delta sigma weight residual 1.244 1.237 0.006 9.30e-03 1.16e+04 4.66e-01 bond pdb=" C GLY A 135 " pdb=" O GLY A 135 " ideal model delta sigma weight residual 1.234 1.242 -0.008 1.20e-02 6.94e+03 4.56e-01 bond pdb=" C LEU C 128 " pdb=" O LEU C 128 " ideal model delta sigma weight residual 1.236 1.244 -0.008 1.15e-02 7.56e+03 4.45e-01 bond pdb=" C GLY C 135 " pdb=" O GLY C 135 " ideal model delta sigma weight residual 1.234 1.241 -0.008 1.20e-02 6.94e+03 4.38e-01 ... (remaining 15995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 21173 1.19 - 2.38: 492 2.38 - 3.58: 140 3.58 - 4.77: 10 4.77 - 5.96: 10 Bond angle restraints: 21825 Sorted by residual: angle pdb=" C PHE E 247 " pdb=" N PHE E 248 " pdb=" CA PHE E 248 " ideal model delta sigma weight residual 121.14 117.58 3.56 1.75e+00 3.27e-01 4.15e+00 angle pdb=" C PHE D 247 " pdb=" N PHE D 248 " pdb=" CA PHE D 248 " ideal model delta sigma weight residual 121.14 117.58 3.56 1.75e+00 3.27e-01 4.13e+00 angle pdb=" C PHE C 247 " pdb=" N PHE C 248 " pdb=" CA PHE C 248 " ideal model delta sigma weight residual 121.14 117.60 3.54 1.75e+00 3.27e-01 4.10e+00 angle pdb=" C PHE B 247 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " ideal model delta sigma weight residual 121.14 117.61 3.53 1.75e+00 3.27e-01 4.06e+00 angle pdb=" C PHE A 247 " pdb=" N PHE A 248 " pdb=" CA PHE A 248 " ideal model delta sigma weight residual 121.14 117.63 3.51 1.75e+00 3.27e-01 4.02e+00 ... (remaining 21820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 8457 15.52 - 31.03: 683 31.03 - 46.55: 100 46.55 - 62.06: 60 62.06 - 77.58: 15 Dihedral angle restraints: 9315 sinusoidal: 3715 harmonic: 5600 Sorted by residual: dihedral pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " pdb=" CG GLN A 74 " pdb=" CD GLN A 74 " ideal model delta sinusoidal sigma weight residual 180.00 124.32 55.68 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA GLN C 74 " pdb=" CB GLN C 74 " pdb=" CG GLN C 74 " pdb=" CD GLN C 74 " ideal model delta sinusoidal sigma weight residual 180.00 124.32 55.68 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA GLN E 74 " pdb=" CB GLN E 74 " pdb=" CG GLN E 74 " pdb=" CD GLN E 74 " ideal model delta sinusoidal sigma weight residual 180.00 124.32 55.68 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1542 0.031 - 0.062: 635 0.062 - 0.094: 142 0.094 - 0.125: 56 0.125 - 0.156: 10 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA PHE B 248 " pdb=" N PHE B 248 " pdb=" C PHE B 248 " pdb=" CB PHE B 248 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE E 232 " pdb=" N ILE E 232 " pdb=" C ILE E 232 " pdb=" CB ILE E 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2382 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 248 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C PHE C 248 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE C 248 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 249 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 248 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C PHE D 248 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE D 248 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 249 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 248 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C PHE E 248 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE E 248 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU E 249 " 0.008 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5184 2.84 - 3.36: 15913 3.36 - 3.87: 30870 3.87 - 4.39: 36708 4.39 - 4.90: 57695 Nonbonded interactions: 146370 Sorted by model distance: nonbonded pdb=" O ASN D 296 " pdb="CA CA D 501 " model vdw 2.329 3.250 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 501 " model vdw 2.357 3.250 nonbonded pdb=" O ASN A 296 " pdb="CA CA A 503 " model vdw 2.359 3.250 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 502 " model vdw 2.405 3.250 nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.407 3.250 ... (remaining 146365 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 213 or resid 215 through 378)) selection = (chain 'B' and (resid 2 through 213 or resid 215 through 378)) selection = (chain 'C' and (resid 2 through 213 or resid 215 through 378)) selection = (chain 'D' and (resid 2 through 213 or resid 215 through 378)) selection = (chain 'E' and (resid 2 through 213 or resid 215 through 378)) } 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=0.36 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: 13.980 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.040 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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 : 0.002 0.021 16000 Z= 0.119 Angle : 0.485 5.961 21825 Z= 0.262 Chirality : 0.038 0.156 2385 Planarity : 0.004 0.033 2740 Dihedral : 12.598 77.577 5705 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.30 % Allowed : 5.11 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.17), residues: 1890 helix: 0.91 (0.14), residues: 1185 sheet: None (None), residues: 0 loop : -0.25 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.015 0.001 TYR B 97 PHE 0.020 0.001 PHE C 248 TRP 0.012 0.001 TRP B 93 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (16000) covalent geometry : angle 0.48485 / 0.26 (21825) hydrogen bonds : bond 0.13089 / 8.21 ( 970) hydrogen bonds : angle 5.67469 / 4.14 ( 2840) *********************** 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 257 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.666 Fit side-chains REVERT: A 344 GLN cc_start: 0.8478 (mt0) cc_final: 0.7947 (mm-40) REVERT: B 344 GLN cc_start: 0.8414 (mt0) cc_final: 0.7628 (tp-100) REVERT: C 41 LEU cc_start: 0.8415 (tp) cc_final: 0.8199 (tp) REVERT: C 344 GLN cc_start: 0.8371 (mt0) cc_final: 0.7584 (tp-100) REVERT: D 72 TYR cc_start: 0.6568 (m-80) cc_final: 0.6252 (m-80) REVERT: D 159 GLN cc_start: 0.8295 (mt0) cc_final: 0.8067 (mt0) REVERT: D 342 GLU cc_start: 0.7885 (tt0) cc_final: 0.7636 (tt0) REVERT: D 344 GLN cc_start: 0.8312 (mt0) cc_final: 0.7852 (mm-40) REVERT: E 163 MET cc_start: 0.8921 (ttp) cc_final: 0.8719 (ttm) REVERT: E 340 LYS cc_start: 0.7212 (mtpt) cc_final: 0.6971 (mtpt) REVERT: E 344 GLN cc_start: 0.8402 (mt0) cc_final: 0.7672 (tp-100) outliers start: 5 outliers final: 5 residues processed: 257 average time/residue: 0.7161 time to fit residues: 201.4738 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN B 95 ASN B 339 ASN C 339 ASN D 95 ASN D 339 ASN E 95 ASN E 339 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.108113 restraints weight = 41000.481| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.57 r_work: 0.2849 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16000 Z= 0.160 Angle : 0.531 6.001 21825 Z= 0.286 Chirality : 0.040 0.156 2385 Planarity : 0.005 0.035 2740 Dihedral : 4.801 44.506 2100 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.54 % Allowed : 8.35 % Favored : 91.11 % 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: 1.21 (0.18), residues: 1890 helix: 1.30 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.05 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 313 TYR 0.021 0.002 TYR D 97 PHE 0.023 0.002 PHE A 248 TRP 0.016 0.002 TRP E 309 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (16000) covalent geometry : angle 0.53103 / 0.29 (21825) hydrogen bonds : bond 0.05821 / 3.74 ( 970) hydrogen bonds : angle 4.75177 / 3.48 ( 2840) *********************** 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 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.669 Fit side-chains REVERT: A 344 GLN cc_start: 0.8857 (mt0) cc_final: 0.8250 (mm-40) REVERT: B 344 GLN cc_start: 0.8647 (mt0) cc_final: 0.7881 (tp-100) REVERT: C 344 GLN cc_start: 0.8604 (mt0) cc_final: 0.7790 (tp-100) REVERT: D 72 TYR cc_start: 0.6746 (m-80) cc_final: 0.6392 (m-80) REVERT: D 344 GLN cc_start: 0.8742 (mt0) cc_final: 0.7873 (tp-100) REVERT: E 344 GLN cc_start: 0.8711 (mt0) cc_final: 0.7903 (tp-100) outliers start: 9 outliers final: 6 residues processed: 229 average time/residue: 0.6958 time to fit residues: 174.8252 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 80 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.0770 chunk 27 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110414 restraints weight = 48823.841| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.25 r_work: 0.2811 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16000 Z= 0.137 Angle : 0.506 6.499 21825 Z= 0.269 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.708 45.590 2100 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.54 % Allowed : 9.01 % Favored : 90.45 % 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: 1.35 (0.18), residues: 1890 helix: 1.46 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.024 0.001 TYR D 97 PHE 0.020 0.001 PHE E 248 TRP 0.015 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (16000) covalent geometry : angle 0.50594 / 0.27 (21825) hydrogen bonds : bond 0.05432 / 3.49 ( 970) hydrogen bonds : angle 4.61478 / 3.39 ( 2840) *********************** 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 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 227 time to evaluate : 0.628 Fit side-chains REVERT: A 344 GLN cc_start: 0.8859 (mt0) cc_final: 0.8195 (mm-40) REVERT: B 344 GLN cc_start: 0.8673 (mt0) cc_final: 0.7815 (tp-100) REVERT: C 340 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6915 (mtpt) REVERT: C 344 GLN cc_start: 0.8641 (mt0) cc_final: 0.7747 (tp-100) REVERT: D 344 GLN cc_start: 0.8750 (mt0) cc_final: 0.7795 (tp-100) REVERT: E 97 TYR cc_start: 0.8381 (t80) cc_final: 0.8158 (t80) REVERT: E 344 GLN cc_start: 0.8726 (mt0) cc_final: 0.7843 (tp-100) outliers start: 9 outliers final: 5 residues processed: 233 average time/residue: 0.6631 time to fit residues: 169.5712 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108483 restraints weight = 34627.002| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.12 r_work: 0.2913 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16000 Z= 0.158 Angle : 0.531 6.806 21825 Z= 0.282 Chirality : 0.040 0.157 2385 Planarity : 0.005 0.038 2740 Dihedral : 4.645 43.422 2098 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.66 % Allowed : 9.19 % Favored : 90.15 % 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: 1.37 (0.18), residues: 1890 helix: 1.47 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.027 0.002 TYR A 97 PHE 0.022 0.002 PHE C 248 TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (16000) covalent geometry : angle 0.53098 / 0.28 (21825) hydrogen bonds : bond 0.05693 / 3.66 ( 970) hydrogen bonds : angle 4.62654 / 3.39 ( 2840) *********************** 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 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 0.644 Fit side-chains REVERT: A 344 GLN cc_start: 0.8791 (mt0) cc_final: 0.8115 (mm-40) REVERT: B 344 GLN cc_start: 0.8649 (mt0) cc_final: 0.7757 (tp-100) REVERT: C 340 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6858 (mtpt) REVERT: C 344 GLN cc_start: 0.8604 (mt0) cc_final: 0.7654 (tp-100) REVERT: D 344 GLN cc_start: 0.8712 (mt0) cc_final: 0.7737 (tp-100) REVERT: E 344 GLN cc_start: 0.8680 (mt0) cc_final: 0.7747 (tp-100) outliers start: 11 outliers final: 7 residues processed: 230 average time/residue: 0.6728 time to fit residues: 169.6820 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 79 optimal weight: 0.3980 chunk 147 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107178 restraints weight = 44751.910| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.23 r_work: 0.2849 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16000 Z= 0.163 Angle : 0.537 7.240 21825 Z= 0.285 Chirality : 0.040 0.157 2385 Planarity : 0.005 0.038 2740 Dihedral : 4.675 43.416 2098 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.48 % Allowed : 9.73 % Favored : 89.79 % 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: 1.36 (0.18), residues: 1890 helix: 1.46 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.029 0.002 TYR A 97 PHE 0.023 0.002 PHE D 248 TRP 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16000) covalent geometry : angle 0.53660 / 0.28 (21825) hydrogen bonds : bond 0.05715 / 3.68 ( 970) hydrogen bonds : angle 4.63370 / 3.40 ( 2840) *********************** 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 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.631 Fit side-chains REVERT: A 344 GLN cc_start: 0.8853 (mt0) cc_final: 0.8129 (mm-40) REVERT: B 344 GLN cc_start: 0.8734 (mt0) cc_final: 0.7757 (tp-100) REVERT: C 344 GLN cc_start: 0.8678 (mt0) cc_final: 0.7656 (tp-100) REVERT: D 344 GLN cc_start: 0.8782 (mt0) cc_final: 0.7715 (tp-100) REVERT: E 344 GLN cc_start: 0.8761 (mt0) cc_final: 0.7739 (tp-100) outliers start: 8 outliers final: 6 residues processed: 225 average time/residue: 0.6876 time to fit residues: 169.7484 Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 GLN B 95 ASN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112946 restraints weight = 39093.456| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.70 r_work: 0.2967 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16000 Z= 0.117 Angle : 0.481 7.450 21825 Z= 0.255 Chirality : 0.037 0.154 2385 Planarity : 0.004 0.035 2740 Dihedral : 4.473 46.260 2098 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.42 % Allowed : 9.97 % Favored : 89.61 % 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: 1.53 (0.18), residues: 1890 helix: 1.61 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.022 0.001 TYR A 97 PHE 0.019 0.001 PHE D 248 TRP 0.014 0.002 TRP C 93 HIS 0.002 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (16000) covalent geometry : angle 0.48058 / 0.25 (21825) hydrogen bonds : bond 0.04983 / 3.20 ( 970) hydrogen bonds : angle 4.49527 / 3.31 ( 2840) *********************** 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 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 0.615 Fit side-chains REVERT: A 344 GLN cc_start: 0.8770 (mt0) cc_final: 0.8079 (mm-40) REVERT: B 344 GLN cc_start: 0.8656 (mt0) cc_final: 0.7718 (tp-100) REVERT: C 64 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7413 (mttp) REVERT: C 344 GLN cc_start: 0.8587 (mt0) cc_final: 0.7597 (tp-100) REVERT: D 344 GLN cc_start: 0.8711 (mt0) cc_final: 0.7676 (tp-100) REVERT: D 356 ARG cc_start: 0.7425 (mmt90) cc_final: 0.7118 (mmt90) REVERT: E 97 TYR cc_start: 0.8272 (t80) cc_final: 0.8071 (t80) REVERT: E 344 GLN cc_start: 0.8686 (mt0) cc_final: 0.7720 (tp-100) outliers start: 7 outliers final: 5 residues processed: 236 average time/residue: 0.6453 time to fit residues: 167.8166 Evaluate side-chains 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104137 restraints weight = 39710.016| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.73 r_work: 0.2820 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16000 Z= 0.230 Angle : 0.606 8.367 21825 Z= 0.322 Chirality : 0.044 0.163 2385 Planarity : 0.005 0.041 2740 Dihedral : 4.777 43.255 2096 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.54 % Allowed : 10.39 % Favored : 89.07 % 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: 1.07 (0.18), residues: 1890 helix: 1.25 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.18 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 125 TYR 0.032 0.002 TYR E 97 PHE 0.027 0.002 PHE B 248 TRP 0.019 0.003 TRP E 309 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (16000) covalent geometry : angle 0.60579 / 0.32 (21825) hydrogen bonds : bond 0.06409 / 4.13 ( 970) hydrogen bonds : angle 4.72627 / 3.46 ( 2840) *********************** 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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 0.545 Fit side-chains REVERT: A 344 GLN cc_start: 0.8819 (mt0) cc_final: 0.8049 (mm-40) REVERT: B 344 GLN cc_start: 0.8725 (mt0) cc_final: 0.7712 (tp-100) REVERT: C 344 GLN cc_start: 0.8674 (mt0) cc_final: 0.7571 (tp-100) REVERT: D 344 GLN cc_start: 0.8771 (mt0) cc_final: 0.7723 (tp-100) REVERT: E 344 GLN cc_start: 0.8770 (mt0) cc_final: 0.7726 (tp-100) outliers start: 9 outliers final: 6 residues processed: 232 average time/residue: 0.6880 time to fit residues: 175.0022 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 129 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN B 95 ASN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109907 restraints weight = 37102.133| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.73 r_work: 0.2852 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16000 Z= 0.147 Angle : 0.523 8.233 21825 Z= 0.277 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.559 44.351 2096 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.42 % Allowed : 10.93 % Favored : 88.65 % 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: 1.36 (0.18), residues: 1890 helix: 1.47 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.029 0.002 TYR D 97 PHE 0.021 0.002 PHE C 248 TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16000) covalent geometry : angle 0.52304 / 0.28 (21825) hydrogen bonds : bond 0.05470 / 3.51 ( 970) hydrogen bonds : angle 4.59763 / 3.38 ( 2840) *********************** 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 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 0.647 Fit side-chains REVERT: A 344 GLN cc_start: 0.8889 (mt0) cc_final: 0.8233 (mm-40) REVERT: B 344 GLN cc_start: 0.8786 (mt0) cc_final: 0.7908 (tp-100) REVERT: C 344 GLN cc_start: 0.8718 (mt0) cc_final: 0.7792 (tp-100) REVERT: D 344 GLN cc_start: 0.8818 (mt0) cc_final: 0.7874 (tp-100) REVERT: E 344 GLN cc_start: 0.8858 (mt0) cc_final: 0.7898 (tp-100) outliers start: 7 outliers final: 7 residues processed: 231 average time/residue: 0.6683 time to fit residues: 169.6529 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107791 restraints weight = 35238.777| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.21 r_work: 0.2907 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16000 Z= 0.162 Angle : 0.542 8.552 21825 Z= 0.287 Chirality : 0.040 0.157 2385 Planarity : 0.005 0.038 2740 Dihedral : 4.591 43.289 2096 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.42 % Allowed : 11.05 % Favored : 88.53 % 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: 1.36 (0.18), residues: 1890 helix: 1.46 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 126 TYR 0.030 0.002 TYR A 97 PHE 0.022 0.002 PHE C 248 TRP 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16000) covalent geometry : angle 0.54218 / 0.29 (21825) hydrogen bonds : bond 0.05694 / 3.66 ( 970) hydrogen bonds : angle 4.61919 / 3.39 ( 2840) *********************** 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 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 0.756 Fit side-chains REVERT: A 344 GLN cc_start: 0.8785 (mt0) cc_final: 0.8081 (mm-40) REVERT: B 344 GLN cc_start: 0.8689 (mt0) cc_final: 0.7746 (tp-100) REVERT: C 344 GLN cc_start: 0.8623 (mt0) cc_final: 0.7611 (tp-100) REVERT: D 344 GLN cc_start: 0.8729 (mt0) cc_final: 0.7724 (tp-100) REVERT: E 344 GLN cc_start: 0.8765 (mt0) cc_final: 0.7733 (tp-100) outliers start: 7 outliers final: 7 residues processed: 228 average time/residue: 0.6769 time to fit residues: 169.4807 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 139 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 149 optimal weight: 0.0870 chunk 145 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108706 restraints weight = 38907.964| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.68 r_work: 0.2891 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16000 Z= 0.150 Angle : 0.532 9.072 21825 Z= 0.281 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.038 2740 Dihedral : 4.546 43.679 2096 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 11.05 % Favored : 88.47 % 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: 1.39 (0.19), residues: 1890 helix: 1.49 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 356 TYR 0.030 0.002 TYR A 97 PHE 0.021 0.002 PHE C 248 TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16000) covalent geometry : angle 0.53215 / 0.28 (21825) hydrogen bonds : bond 0.05526 / 3.55 ( 970) hydrogen bonds : angle 4.59496 / 3.38 ( 2840) ********************** 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 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.681 Fit side-chains REVERT: A 344 GLN cc_start: 0.8833 (mt0) cc_final: 0.8105 (mm-40) REVERT: B 344 GLN cc_start: 0.8713 (mt0) cc_final: 0.7757 (tp-100) REVERT: C 344 GLN cc_start: 0.8645 (mt0) cc_final: 0.7633 (tp-100) REVERT: D 344 GLN cc_start: 0.8739 (mt0) cc_final: 0.7724 (tp-100) REVERT: D 356 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7202 (mmt90) REVERT: E 344 GLN cc_start: 0.8788 (mt0) cc_final: 0.7741 (tp-100) outliers start: 8 outliers final: 7 residues processed: 228 average time/residue: 0.6805 time to fit residues: 170.3057 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 72 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 137 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 GLN B 95 ASN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109589 restraints weight = 38848.314| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.69 r_work: 0.2918 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16000 Z= 0.139 Angle : 0.523 9.399 21825 Z= 0.276 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.492 44.029 2096 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.42 % Allowed : 11.11 % Favored : 88.47 % 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: 1.43 (0.19), residues: 1890 helix: 1.53 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 356 TYR 0.028 0.001 TYR A 97 PHE 0.020 0.001 PHE C 248 TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16000) covalent geometry : angle 0.52328 / 0.28 (21825) hydrogen bonds : bond 0.05385 / 3.46 ( 970) hydrogen bonds : angle 4.56312 / 3.35 ( 2840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6282.49 seconds wall clock time: 108 minutes 5.91 seconds (6485.91 seconds total)