Starting phenix.real_space_refine on Sat May 17 12:39:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egs_47996/05_2025/9egs_47996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egs_47996/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9egs_47996/05_2025/9egs_47996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egs_47996/05_2025/9egs_47996.map" model { file = "/net/cci-nas-00/data/ceres_data/9egs_47996/05_2025/9egs_47996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egs_47996/05_2025/9egs_47996.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.66, per 1000 atoms: 1.05 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: 3.71 Conformation dependent library (CDL) restraints added in 3.4 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: 1.91 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: 5.20 Time building geometry restraints manager: 4.32 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: 0.03 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: 13.830 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 46.020 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.120 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.012 0.001 TRP B 93 HIS 0.003 0.001 HIS A 326 PHE 0.020 0.001 PHE C 248 TYR 0.015 0.001 TYR B 97 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.13089 ( 970) hydrogen bonds : angle 5.67469 ( 2840) covalent geometry : bond 0.00228 (16000) covalent geometry : angle 0.48485 (21825) *********************** 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 : 1.634 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: 1.4763 time to fit residues: 414.1495 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 : 1.765 ------------------------------------------------------------------------------- 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 156 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.136549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109038 restraints weight = 36810.123| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.74 r_work: 0.2819 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16000 Z= 0.167 Angle : 0.541 6.150 21825 Z= 0.291 Chirality : 0.041 0.157 2385 Planarity : 0.005 0.035 2740 Dihedral : 4.844 44.339 2100 Min Nonbonded Distance : 2.281 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 1890 helix: 1.30 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.005 0.001 HIS A 326 PHE 0.024 0.002 PHE A 248 TYR 0.022 0.002 TYR D 97 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05937 ( 970) hydrogen bonds : angle 4.76974 ( 2840) covalent geometry : bond 0.00372 (16000) covalent geometry : angle 0.54135 (21825) *********************** 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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 1.695 Fit side-chains REVERT: A 344 GLN cc_start: 0.8916 (mt0) cc_final: 0.8277 (mm-40) REVERT: B 344 GLN cc_start: 0.8739 (mt0) cc_final: 0.7906 (tp-100) REVERT: C 344 GLN cc_start: 0.8692 (mt0) cc_final: 0.7809 (tp-100) REVERT: D 344 GLN cc_start: 0.8831 (mt0) cc_final: 0.7896 (tp-100) REVERT: E 344 GLN cc_start: 0.8781 (mt0) cc_final: 0.7914 (tp-100) outliers start: 9 outliers final: 6 residues processed: 230 average time/residue: 1.4772 time to fit residues: 371.7930 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 : 1.815 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.138138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108850 restraints weight = 43830.415| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.78 r_work: 0.2840 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1087 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 : 0.511 6.343 21825 Z= 0.271 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.748 45.267 2100 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.54 % Allowed : 9.07 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 1890 helix: 1.48 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.020 0.001 PHE E 248 TYR 0.025 0.001 TYR D 97 ARG 0.002 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 970) hydrogen bonds : angle 4.63559 ( 2840) covalent geometry : bond 0.00300 (16000) covalent geometry : angle 0.51058 (21825) *********************** 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: 9 poor density : 225 time to evaluate : 1.624 Fit side-chains REVERT: A 344 GLN cc_start: 0.8881 (mt0) cc_final: 0.8260 (mm-40) REVERT: B 344 GLN cc_start: 0.8674 (mt0) cc_final: 0.7870 (tp-100) REVERT: C 340 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: C 344 GLN cc_start: 0.8646 (mt0) cc_final: 0.7800 (tp-100) REVERT: D 344 GLN cc_start: 0.8771 (mt0) cc_final: 0.7866 (tp-100) REVERT: E 344 GLN cc_start: 0.8736 (mt0) cc_final: 0.7880 (tp-100) outliers start: 9 outliers final: 5 residues processed: 231 average time/residue: 1.4053 time to fit residues: 355.6852 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 : 1.630 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.135647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.106551 restraints weight = 40575.451| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.01 r_work: 0.2850 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 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 = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16000 Z= 0.174 Angle : 0.552 6.620 21825 Z= 0.293 Chirality : 0.041 0.158 2385 Planarity : 0.005 0.038 2740 Dihedral : 4.747 42.935 2098 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.60 % Allowed : 9.37 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 1890 helix: 1.45 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.005 0.001 HIS A 326 PHE 0.024 0.002 PHE C 248 TYR 0.029 0.002 TYR A 97 ARG 0.002 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.05925 ( 970) hydrogen bonds : angle 4.67480 ( 2840) covalent geometry : bond 0.00391 (16000) covalent geometry : angle 0.55225 (21825) *********************** 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 1.654 Fit side-chains REVERT: A 344 GLN cc_start: 0.8833 (mt0) cc_final: 0.8057 (mm-40) REVERT: B 344 GLN cc_start: 0.8694 (mt0) cc_final: 0.7714 (tp-100) REVERT: C 340 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6807 (mtpt) REVERT: C 344 GLN cc_start: 0.8626 (mt0) cc_final: 0.7606 (tp-100) REVERT: D 344 GLN cc_start: 0.8743 (mt0) cc_final: 0.7696 (tp-100) REVERT: E 344 GLN cc_start: 0.8707 (mt0) cc_final: 0.7700 (tp-100) outliers start: 10 outliers final: 6 residues processed: 227 average time/residue: 1.4440 time to fit residues: 358.6344 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 132 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.137095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108140 restraints weight = 45379.905| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.97 r_work: 0.2784 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1230 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= 0.146 Angle : 0.521 7.291 21825 Z= 0.276 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.663 43.965 2098 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 1890 helix: 1.52 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.022 0.001 PHE D 248 TYR 0.029 0.002 TYR A 97 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 970) hydrogen bonds : angle 4.61752 ( 2840) covalent geometry : bond 0.00320 (16000) covalent geometry : angle 0.52069 (21825) *********************** 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.627 Fit side-chains REVERT: A 344 GLN cc_start: 0.8895 (mt0) cc_final: 0.8196 (mm-40) REVERT: B 344 GLN cc_start: 0.8728 (mt0) cc_final: 0.7850 (tp-100) REVERT: C 344 GLN cc_start: 0.8695 (mt0) cc_final: 0.7764 (tp-100) REVERT: D 344 GLN cc_start: 0.8804 (mt0) cc_final: 0.7815 (tp-100) REVERT: E 344 GLN cc_start: 0.8779 (mt0) cc_final: 0.7836 (tp-100) outliers start: 8 outliers final: 6 residues processed: 229 average time/residue: 1.4728 time to fit residues: 368.7909 Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 105 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.139477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110806 restraints weight = 41229.659| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.01 r_work: 0.2914 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16000 Z= 0.125 Angle : 0.493 7.995 21825 Z= 0.260 Chirality : 0.038 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.537 45.203 2098 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.42 % Allowed : 10.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 1890 helix: 1.54 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 93 HIS 0.003 0.001 HIS A 326 PHE 0.018 0.001 PHE C 248 TYR 0.024 0.001 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 970) hydrogen bonds : angle 4.53305 ( 2840) covalent geometry : bond 0.00262 (16000) covalent geometry : angle 0.49258 (21825) *********************** 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 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 1.706 Fit side-chains REVERT: A 344 GLN cc_start: 0.8793 (mt0) cc_final: 0.8073 (mm-40) REVERT: B 344 GLN cc_start: 0.8661 (mt0) cc_final: 0.7701 (tp-100) REVERT: C 344 GLN cc_start: 0.8588 (mt0) cc_final: 0.7575 (tp-100) REVERT: D 344 GLN cc_start: 0.8697 (mt0) cc_final: 0.7638 (tp-100) REVERT: D 356 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7082 (mmt90) REVERT: E 97 TYR cc_start: 0.8288 (t80) cc_final: 0.8038 (t80) REVERT: E 344 GLN cc_start: 0.8681 (mt0) cc_final: 0.7688 (tp-100) outliers start: 7 outliers final: 6 residues processed: 224 average time/residue: 1.4074 time to fit residues: 346.4812 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 38 optimal weight: 0.0370 chunk 52 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106895 restraints weight = 40340.610| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.65 r_work: 0.2846 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16000 Z= 0.163 Angle : 0.540 8.475 21825 Z= 0.286 Chirality : 0.040 0.156 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.662 42.989 2098 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.27 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 1890 helix: 1.57 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.022 0.002 PHE E 248 TYR 0.028 0.002 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05713 ( 970) hydrogen bonds : angle 4.60645 ( 2840) covalent geometry : bond 0.00367 (16000) covalent geometry : angle 0.53951 (21825) *********************** 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 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.834 Fit side-chains REVERT: A 344 GLN cc_start: 0.8860 (mt0) cc_final: 0.8211 (mm-40) REVERT: B 344 GLN cc_start: 0.8706 (mt0) cc_final: 0.7879 (tp-100) REVERT: C 344 GLN cc_start: 0.8660 (mt0) cc_final: 0.7777 (tp-100) REVERT: D 203 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8466 (t70) REVERT: D 344 GLN cc_start: 0.8770 (mt0) cc_final: 0.7828 (tp-100) REVERT: E 344 GLN cc_start: 0.8773 (mt0) cc_final: 0.7865 (tp-100) outliers start: 8 outliers final: 6 residues processed: 222 average time/residue: 1.4564 time to fit residues: 354.9552 Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.136525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107204 restraints weight = 41223.860| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.95 r_work: 0.2870 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16000 Z= 0.157 Angle : 0.536 8.972 21825 Z= 0.283 Chirality : 0.040 0.156 2385 Planarity : 0.004 0.038 2740 Dihedral : 4.669 43.462 2098 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 1890 helix: 1.55 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.022 0.002 PHE C 248 TYR 0.030 0.002 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 970) hydrogen bonds : angle 4.60122 ( 2840) covalent geometry : bond 0.00351 (16000) covalent geometry : angle 0.53577 (21825) *********************** 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 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.674 Fit side-chains REVERT: A 344 GLN cc_start: 0.8860 (mt0) cc_final: 0.8114 (mm-40) REVERT: B 344 GLN cc_start: 0.8749 (mt0) cc_final: 0.7754 (tp-100) REVERT: C 344 GLN cc_start: 0.8675 (mt0) cc_final: 0.7657 (tp-100) REVERT: D 203 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8516 (t70) REVERT: D 344 GLN cc_start: 0.8768 (mt0) cc_final: 0.7713 (tp-100) REVERT: E 344 GLN cc_start: 0.8776 (mt0) cc_final: 0.7756 (tp-100) outliers start: 8 outliers final: 7 residues processed: 227 average time/residue: 1.4187 time to fit residues: 352.7122 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 : 1.588 ------------------------------------------------------------------------------- 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 D residue 203 ASP 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 99 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 131 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 101 optimal weight: 0.0020 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.140679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112429 restraints weight = 33908.481| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.02 r_work: 0.2982 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 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: 0.8609 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16000 Z= 0.118 Angle : 0.490 8.772 21825 Z= 0.258 Chirality : 0.037 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.485 45.901 2098 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.54 % Allowed : 10.51 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 1890 helix: 1.62 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.09 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 93 HIS 0.003 0.001 HIS A 326 PHE 0.017 0.001 PHE D 248 TYR 0.022 0.001 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 970) hydrogen bonds : angle 4.50164 ( 2840) covalent geometry : bond 0.00245 (16000) covalent geometry : angle 0.48989 (21825) *********************** 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 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 2.048 Fit side-chains REVERT: A 344 GLN cc_start: 0.8784 (mt0) cc_final: 0.8124 (mm-40) REVERT: B 344 GLN cc_start: 0.8649 (mt0) cc_final: 0.7749 (tp-100) REVERT: C 344 GLN cc_start: 0.8577 (mt0) cc_final: 0.7642 (tp-100) REVERT: C 356 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7263 (mmt90) REVERT: D 344 GLN cc_start: 0.8714 (mt0) cc_final: 0.7715 (tp-100) REVERT: D 356 ARG cc_start: 0.7458 (mmt90) cc_final: 0.7197 (mmt90) REVERT: E 97 TYR cc_start: 0.8185 (t80) cc_final: 0.7954 (t80) REVERT: E 344 GLN cc_start: 0.8694 (mt0) cc_final: 0.7722 (tp-100) outliers start: 9 outliers final: 6 residues processed: 221 average time/residue: 1.3961 time to fit residues: 338.9190 Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 214 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 56 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106742 restraints weight = 38390.687| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.66 r_work: 0.2867 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16000 Z= 0.167 Angle : 0.554 9.571 21825 Z= 0.292 Chirality : 0.040 0.156 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.567 42.947 2096 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.36 % Allowed : 10.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1890 helix: 1.59 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.10 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.022 0.002 PHE E 248 TYR 0.026 0.002 TYR B 97 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05767 ( 970) hydrogen bonds : angle 4.59804 ( 2840) covalent geometry : bond 0.00376 (16000) covalent geometry : angle 0.55366 (21825) ********************** 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 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 1.601 Fit side-chains REVERT: A 344 GLN cc_start: 0.8818 (mt0) cc_final: 0.8055 (mm-40) REVERT: B 344 GLN cc_start: 0.8701 (mt0) cc_final: 0.7710 (tp-100) REVERT: C 344 GLN cc_start: 0.8651 (mt0) cc_final: 0.7614 (tp-100) REVERT: D 344 GLN cc_start: 0.8730 (mt0) cc_final: 0.7667 (tp-100) REVERT: E 245 TYR cc_start: 0.7835 (m-80) cc_final: 0.7487 (m-80) REVERT: E 344 GLN cc_start: 0.8742 (mt0) cc_final: 0.7698 (tp-100) outliers start: 6 outliers final: 6 residues processed: 223 average time/residue: 1.4159 time to fit residues: 347.4003 Evaluate side-chains 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 5 optimal weight: 0.0570 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.138004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108848 restraints weight = 34341.849| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.11 r_work: 0.2934 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1340 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= 0.138 Angle : 0.525 9.653 21825 Z= 0.276 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.483 44.137 2096 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 1890 helix: 1.61 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 PHE 0.020 0.001 PHE D 248 TYR 0.027 0.001 TYR A 97 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05367 ( 970) hydrogen bonds : angle 4.55334 ( 2840) covalent geometry : bond 0.00301 (16000) covalent geometry : angle 0.52545 (21825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12750.36 seconds wall clock time: 220 minutes 27.57 seconds (13227.57 seconds total)