Starting phenix.real_space_refine on Thu Sep 18 09:24:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egs_47996/09_2025/9egs_47996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egs_47996/09_2025/9egs_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_47996/09_2025/9egs_47996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egs_47996/09_2025/9egs_47996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9egs_47996/09_2025/9egs_47996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egs_47996/09_2025/9egs_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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 6.92, per 1000 atoms: 0.44 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: 1.56 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.76 Time building geometry restraints manager: 2.02 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 2.510 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 501 " model vdw 2.357 2.510 nonbonded pdb=" O ASN A 296 " pdb="CA CA A 503 " model vdw 2.359 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 502 " model vdw 2.405 2.510 nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.407 2.510 ... (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: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 19.830 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 aren 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 covalent geometry : bond 0.00228 (16000) covalent geometry : angle 0.48485 (21825) hydrogen bonds : bond 0.13089 ( 970) hydrogen bonds : angle 5.67469 ( 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 : 0.645 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: 0.8401 (mt0) cc_final: 0.7672 (tp-100) outliers start: 5 outliers final: 5 residues processed: 257 average time/residue: 0.7347 time to fit residues: 205.3597 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 : 0.707 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3482 r_free = 0.3482 target = 0.137033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108194 restraints weight = 40871.069| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.11 r_work: 0.2869 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0984 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 : 0.532 6.022 21825 Z= 0.286 Chirality : 0.040 0.156 2385 Planarity : 0.005 0.035 2740 Dihedral : 4.820 44.615 2100 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 8.41 % 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 aren not related in a simple way. whole: 1.24 (0.18), residues: 1890 helix: 1.33 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.06 (0.23), 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 covalent geometry : bond 0.00353 (16000) covalent geometry : angle 0.53221 (21825) hydrogen bonds : bond 0.05824 ( 970) hydrogen bonds : angle 4.74766 ( 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: 8 poor density : 225 time to evaluate : 0.628 Fit side-chains REVERT: A 344 GLN cc_start: 0.8788 (mt0) cc_final: 0.8049 (mm-40) REVERT: B 344 GLN cc_start: 0.8618 (mt0) cc_final: 0.7681 (tp-100) REVERT: C 159 GLN cc_start: 0.8349 (mt0) cc_final: 0.8087 (mt0) REVERT: C 344 GLN cc_start: 0.8573 (mt0) cc_final: 0.7575 (tp-100) REVERT: D 344 GLN cc_start: 0.8674 (mt0) cc_final: 0.7659 (tp-100) REVERT: E 344 GLN cc_start: 0.8650 (mt0) cc_final: 0.7699 (tp-100) outliers start: 8 outliers final: 5 residues processed: 230 average time/residue: 0.7277 time to fit residues: 182.6473 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 78 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3493 r_free = 0.3493 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110478 restraints weight = 48589.735| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.69 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1103 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= 0.144 Angle : 0.517 6.531 21825 Z= 0.274 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.647 44.473 2098 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.60 % Allowed : 8.95 % 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 aren 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 A 313 TYR 0.025 0.002 TYR D 97 PHE 0.020 0.001 PHE E 248 TRP 0.015 0.002 TRP E 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00313 (16000) covalent geometry : angle 0.51711 (21825) hydrogen bonds : bond 0.05547 ( 970) hydrogen bonds : angle 4.63633 ( 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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.631 Fit side-chains REVERT: B 344 GLN cc_start: 0.8130 (mt0) cc_final: 0.7801 (tp-100) REVERT: C 340 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6851 (mtpt) REVERT: C 344 GLN cc_start: 0.8076 (mt0) cc_final: 0.7694 (tp-100) REVERT: D 344 GLN cc_start: 0.8097 (mt0) cc_final: 0.7712 (tp-100) REVERT: E 344 GLN cc_start: 0.8150 (mt0) cc_final: 0.7739 (tp-100) outliers start: 10 outliers final: 6 residues processed: 230 average time/residue: 0.7074 time to fit residues: 178.1884 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 : 0.502 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 66 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 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: 1.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3984 r_free = 0.3984 target = 0.163762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135292 restraints weight = 35978.756| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.52 r_work: 0.3064 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16000 Z= 0.207 Angle : 0.586 6.732 21825 Z= 0.311 Chirality : 0.043 0.159 2385 Planarity : 0.005 0.040 2740 Dihedral : 4.871 43.115 2098 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.60 % Allowed : 9.19 % Favored : 90.21 % 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 aren not related in a simple way. whole: 1.06 (0.18), residues: 1890 helix: 1.24 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.19 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 125 TYR 0.032 0.002 TYR A 97 PHE 0.026 0.002 PHE E 248 TRP 0.018 0.002 TRP C 309 HIS 0.006 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00478 (16000) covalent geometry : angle 0.58643 (21825) hydrogen bonds : bond 0.06273 ( 970) hydrogen bonds : angle 4.74025 ( 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 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.616 Fit side-chains REVERT: B 344 GLN cc_start: 0.8592 (mt0) cc_final: 0.7624 (tp-100) REVERT: C 340 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6783 (mtpt) REVERT: C 344 GLN cc_start: 0.8574 (mt0) cc_final: 0.7502 (tp-100) REVERT: D 344 GLN cc_start: 0.8658 (mt0) cc_final: 0.7619 (tp-100) REVERT: E 344 GLN cc_start: 0.8640 (mt0) cc_final: 0.7630 (tp-100) outliers start: 10 outliers final: 6 residues processed: 229 average time/residue: 0.7425 time to fit residues: 185.4418 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 : 0.630 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 147 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107571 restraints weight = 44241.404| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.61 r_work: 0.2792 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 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 = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1257 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= 0.149 Angle : 0.528 7.488 21825 Z= 0.279 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.705 44.156 2098 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 aren 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 A 126 TYR 0.029 0.002 TYR D 97 PHE 0.022 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 covalent geometry : bond 0.00329 (16000) covalent geometry : angle 0.52757 (21825) hydrogen bonds : bond 0.05577 ( 970) hydrogen bonds : angle 4.63377 ( 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 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.409 Fit side-chains REVERT: A 344 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: B 344 GLN cc_start: 0.8774 (mt0) cc_final: 0.7884 (tp-100) REVERT: C 340 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6884 (mtpt) REVERT: C 344 GLN cc_start: 0.8726 (mt0) cc_final: 0.7783 (tp-100) REVERT: D 344 GLN cc_start: 0.8833 (mt0) cc_final: 0.7856 (tp-100) REVERT: E 344 GLN cc_start: 0.8823 (mt0) cc_final: 0.7873 (tp-100) outliers start: 8 outliers final: 6 residues processed: 227 average time/residue: 0.6836 time to fit residues: 169.5917 Evaluate side-chains 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 344 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110898 restraints weight = 38740.123| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.73 r_work: 0.2840 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1262 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 : 0.512 7.959 21825 Z= 0.270 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.623 44.358 2098 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.21 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.18), residues: 1890 helix: 1.56 (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 0.003 0.000 ARG C 356 TYR 0.027 0.001 TYR A 97 PHE 0.019 0.001 PHE A 248 TRP 0.016 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00295 (16000) covalent geometry : angle 0.51176 (21825) hydrogen bonds : bond 0.05374 ( 970) hydrogen bonds : angle 4.58418 ( 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 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.591 Fit side-chains REVERT: A 344 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: B 344 GLN cc_start: 0.8779 (mt0) cc_final: 0.7948 (tp-100) REVERT: C 344 GLN cc_start: 0.8727 (mt0) cc_final: 0.7847 (tp-100) REVERT: D 344 GLN cc_start: 0.8830 (mt0) cc_final: 0.7898 (tp-100) REVERT: E 344 GLN cc_start: 0.8827 (mt0) cc_final: 0.7944 (tp-100) outliers start: 8 outliers final: 6 residues processed: 221 average time/residue: 0.6960 time to fit residues: 168.4671 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 344 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 71 optimal weight: 0.0040 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108304 restraints weight = 39454.228| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.81 r_work: 0.2885 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1266 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= 0.144 Angle : 0.523 8.525 21825 Z= 0.276 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.038 2740 Dihedral : 4.624 43.773 2098 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.60 % Allowed : 10.33 % 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 aren not related in a simple way. whole: 1.49 (0.18), residues: 1890 helix: 1.57 (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 0.028 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 covalent geometry : bond 0.00317 (16000) covalent geometry : angle 0.52254 (21825) hydrogen bonds : bond 0.05481 ( 970) hydrogen bonds : angle 4.57867 ( 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 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.629 Fit side-chains REVERT: A 344 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: B 344 GLN cc_start: 0.8683 (mt0) cc_final: 0.7697 (tp-100) REVERT: C 344 GLN cc_start: 0.8624 (mt0) cc_final: 0.7579 (tp-100) REVERT: D 203 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8464 (t70) REVERT: D 344 GLN cc_start: 0.8723 (mt0) cc_final: 0.7657 (tp-100) REVERT: E 344 GLN cc_start: 0.8708 (mt0) cc_final: 0.7683 (tp-100) outliers start: 10 outliers final: 6 residues processed: 221 average time/residue: 0.7278 time to fit residues: 175.9208 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 344 GLN 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 D residue 203 ASP 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: 0.5980 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 184 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109616 restraints weight = 36925.229| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.20 r_work: 0.2880 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16000 Z= 0.131 Angle : 0.506 9.095 21825 Z= 0.267 Chirality : 0.038 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.553 44.624 2098 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 10.57 % Favored : 88.89 % 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 aren not related in a simple way. whole: 1.49 (0.18), residues: 1890 helix: 1.54 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.025 0.001 TYR A 97 PHE 0.018 0.001 PHE E 248 TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00280 (16000) covalent geometry : angle 0.50644 (21825) hydrogen bonds : bond 0.05261 ( 970) hydrogen bonds : angle 4.53106 ( 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 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.628 Fit side-chains REVERT: A 344 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: B 344 GLN cc_start: 0.8703 (mt0) cc_final: 0.7909 (tp-100) REVERT: C 344 GLN cc_start: 0.8659 (mt0) cc_final: 0.7811 (tp-100) REVERT: D 344 GLN cc_start: 0.8781 (mt0) cc_final: 0.7869 (tp-100) REVERT: D 356 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7250 (mmt90) REVERT: E 344 GLN cc_start: 0.8760 (mt0) cc_final: 0.7909 (tp-100) outliers start: 9 outliers final: 7 residues processed: 224 average time/residue: 0.6860 time to fit residues: 168.3978 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 344 GLN 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: 5.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 155 GLN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.136292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108542 restraints weight = 35182.069| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.63 r_work: 0.2831 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1334 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 : 0.542 8.607 21825 Z= 0.286 Chirality : 0.040 0.156 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.657 43.075 2098 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.60 % Allowed : 10.63 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 1890 helix: 1.56 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.027 0.002 TYR A 97 PHE 0.021 0.002 PHE E 248 TRP 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00359 (16000) covalent geometry : angle 0.54157 (21825) hydrogen bonds : bond 0.05679 ( 970) hydrogen bonds : angle 4.59802 ( 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 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.595 Fit side-chains REVERT: B 344 GLN cc_start: 0.8764 (mt0) cc_final: 0.7905 (tp-100) REVERT: C 344 GLN cc_start: 0.8738 (mt0) cc_final: 0.7811 (tp-100) REVERT: D 344 GLN cc_start: 0.8826 (mt0) cc_final: 0.7866 (tp-100) REVERT: E 344 GLN cc_start: 0.8812 (mt0) cc_final: 0.7894 (tp-100) outliers start: 10 outliers final: 7 residues processed: 225 average time/residue: 0.7491 time to fit residues: 183.8746 Evaluate side-chains 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 149 optimal weight: 0.0270 chunk 145 optimal weight: 0.0020 chunk 22 optimal weight: 2.9990 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3507 r_free = 0.3507 target = 0.139115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110243 restraints weight = 38805.287| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.20 r_work: 0.2878 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16000 Z= 0.127 Angle : 0.505 9.071 21825 Z= 0.266 Chirality : 0.038 0.155 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.536 45.026 2098 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.48 % Allowed : 10.93 % Favored : 88.59 % 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 aren not related in a simple way. whole: 1.51 (0.19), residues: 1890 helix: 1.56 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.024 0.001 TYR A 97 PHE 0.018 0.001 PHE C 248 TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00271 (16000) covalent geometry : angle 0.50538 (21825) hydrogen bonds : bond 0.05184 ( 970) hydrogen bonds : angle 4.53147 ( 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 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.626 Fit side-chains REVERT: B 344 GLN cc_start: 0.8721 (mt0) cc_final: 0.7921 (tp-100) REVERT: C 344 GLN cc_start: 0.8675 (mt0) cc_final: 0.7831 (tp-100) REVERT: C 356 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7321 (mmt90) REVERT: D 344 GLN cc_start: 0.8800 (mt0) cc_final: 0.7893 (tp-100) REVERT: D 356 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7328 (mmt90) REVERT: E 97 TYR cc_start: 0.8250 (t80) cc_final: 0.7982 (t80) REVERT: E 344 GLN cc_start: 0.8781 (mt0) cc_final: 0.7931 (tp-100) outliers start: 8 outliers final: 7 residues processed: 227 average time/residue: 0.6919 time to fit residues: 172.0663 Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 0.0170 chunk 42 optimal weight: 0.0060 chunk 113 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 137 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3519 r_free = 0.3519 target = 0.140206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111320 restraints weight = 38813.325| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.20 r_work: 0.2893 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16000 Z= 0.121 Angle : 0.498 9.512 21825 Z= 0.261 Chirality : 0.038 0.154 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.469 45.502 2098 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.42 % Allowed : 10.99 % Favored : 88.59 % 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 aren not related in a simple way. whole: 1.59 (0.19), residues: 1890 helix: 1.63 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.022 0.001 TYR A 33 PHE 0.017 0.001 PHE D 248 TRP 0.015 0.002 TRP C 93 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00254 (16000) covalent geometry : angle 0.49801 (21825) hydrogen bonds : bond 0.05070 ( 970) hydrogen bonds : angle 4.49305 ( 2840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5962.65 seconds wall clock time: 102 minutes 25.73 seconds (6145.73 seconds total)