Starting phenix.real_space_refine on Sat Jun 14 02:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egs_47996/06_2025/9egs_47996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egs_47996/06_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_47996/06_2025/9egs_47996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egs_47996/06_2025/9egs_47996.map" model { file = "/net/cci-nas-00/data/ceres_data/9egs_47996/06_2025/9egs_47996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egs_47996/06_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-5710/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: 19.37, per 1000 atoms: 1.23 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: 4.19 Conformation dependent library (CDL) restraints added in 3.9 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: 1.68 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: 4.93 Time building geometry restraints manager: 4.93 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: 191.010 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 50.200 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.690 ------------------------------------------------------------------------------- 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 : 1.704 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: 1.6386 time to fit residues: 458.4094 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 : 2.282 ------------------------------------------------------------------------------- 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 = 0.109037 restraints weight = 36810.122| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.74 r_work: 0.2820 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- 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 : 1.579 Fit side-chains REVERT: A 344 GLN cc_start: 0.8909 (mt0) cc_final: 0.8274 (mm-40) REVERT: B 344 GLN cc_start: 0.8727 (mt0) cc_final: 0.7901 (tp-100) REVERT: C 344 GLN cc_start: 0.8681 (mt0) cc_final: 0.7805 (tp-100) REVERT: D 344 GLN cc_start: 0.8817 (mt0) cc_final: 0.7887 (tp-100) REVERT: E 344 GLN cc_start: 0.8768 (mt0) cc_final: 0.7907 (tp-100) outliers start: 9 outliers final: 6 residues processed: 230 average time/residue: 1.9184 time to fit residues: 483.0440 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 : 2.327 ------------------------------------------------------------------------------- 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: 0.9990 chunk 170 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 108 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109333 restraints weight = 43859.826| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.79 r_work: 0.2846 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1089 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= 0.135 Angle : 0.504 6.498 21825 Z= 0.268 Chirality : 0.039 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.725 45.750 2100 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.54 % Allowed : 9.01 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.18), residues: 1890 helix: 1.49 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile 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 0.024 0.001 TYR D 97 ARG 0.002 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 970) hydrogen bonds : angle 4.61620 ( 2840) covalent geometry : bond 0.00289 (16000) covalent geometry : angle 0.50445 (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 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 227 time to evaluate : 1.630 Fit side-chains REVERT: A 344 GLN cc_start: 0.8876 (mt0) cc_final: 0.8255 (mm-40) REVERT: B 344 GLN cc_start: 0.8667 (mt0) cc_final: 0.7863 (tp-100) REVERT: C 340 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6947 (mtpt) REVERT: C 344 GLN cc_start: 0.8644 (mt0) cc_final: 0.7798 (tp-100) REVERT: D 344 GLN cc_start: 0.8763 (mt0) cc_final: 0.7864 (tp-100) REVERT: E 97 TYR cc_start: 0.8352 (t80) cc_final: 0.8128 (t80) REVERT: E 344 GLN cc_start: 0.8725 (mt0) cc_final: 0.7874 (tp-100) outliers start: 9 outliers final: 5 residues processed: 233 average time/residue: 1.5075 time to fit residues: 384.1267 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 : 1.861 ------------------------------------------------------------------------------- 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: 0.5980 chunk 124 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 140 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107748 restraints weight = 40581.631| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.96 r_work: 0.2870 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16000 Z= 0.155 Angle : 0.529 6.676 21825 Z= 0.281 Chirality : 0.040 0.156 2385 Planarity : 0.004 0.037 2740 Dihedral : 4.655 43.554 2098 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 : 0.60 % Allowed : 9.55 % Favored : 89.85 % 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: 1.51 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.04 (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 C 248 TYR 0.026 0.002 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 970) hydrogen bonds : angle 4.62544 ( 2840) covalent geometry : bond 0.00346 (16000) covalent geometry : angle 0.52922 (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 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 1.868 Fit side-chains REVERT: A 344 GLN cc_start: 0.8804 (mt0) cc_final: 0.8048 (mm-40) REVERT: B 344 GLN cc_start: 0.8673 (mt0) cc_final: 0.7689 (tp-100) REVERT: C 340 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6750 (mtpt) REVERT: C 344 GLN cc_start: 0.8605 (mt0) cc_final: 0.7568 (tp-100) REVERT: D 344 GLN cc_start: 0.8716 (mt0) cc_final: 0.7660 (tp-100) REVERT: E 344 GLN cc_start: 0.8679 (mt0) cc_final: 0.7664 (tp-100) outliers start: 10 outliers final: 6 residues processed: 226 average time/residue: 1.5122 time to fit residues: 374.5560 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 : 2.323 ------------------------------------------------------------------------------- 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: 1.9990 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.135791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106628 restraints weight = 45328.637| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.99 r_work: 0.2758 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16000 Z= 0.171 Angle : 0.549 7.093 21825 Z= 0.291 Chirality : 0.041 0.157 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.733 43.201 2098 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.54 % Allowed : 9.73 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.18), residues: 1890 helix: 1.46 (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 C 309 HIS 0.004 0.001 HIS A 326 PHE 0.023 0.002 PHE D 248 TYR 0.030 0.002 TYR A 97 ARG 0.002 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 970) hydrogen bonds : angle 4.66080 ( 2840) covalent geometry : bond 0.00386 (16000) covalent geometry : angle 0.54913 (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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 2.514 Fit side-chains REVERT: A 344 GLN cc_start: 0.8923 (mt0) cc_final: 0.8220 (mm-40) REVERT: B 344 GLN cc_start: 0.8763 (mt0) cc_final: 0.7867 (tp-100) REVERT: C 340 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6877 (mtpt) REVERT: C 344 GLN cc_start: 0.8727 (mt0) cc_final: 0.7784 (tp-100) REVERT: D 344 GLN cc_start: 0.8828 (mt0) cc_final: 0.7850 (tp-100) REVERT: E 344 GLN cc_start: 0.8809 (mt0) cc_final: 0.7862 (tp-100) outliers start: 9 outliers final: 6 residues processed: 231 average time/residue: 2.0506 time to fit residues: 520.4326 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 : 2.470 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 151 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.139455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110503 restraints weight = 41227.552| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.95 r_work: 0.2909 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 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 = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16000 Z= 0.126 Angle : 0.496 8.257 21825 Z= 0.262 Chirality : 0.038 0.155 2385 Planarity : 0.004 0.036 2740 Dihedral : 4.548 45.400 2098 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 10.15 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.18), residues: 1890 helix: 1.59 (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 0.014 0.002 TRP C 93 HIS 0.003 0.001 HIS A 326 PHE 0.020 0.001 PHE D 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 0.05174 ( 970) hydrogen bonds : angle 4.53926 ( 2840) covalent geometry : bond 0.00265 (16000) covalent geometry : angle 0.49559 (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 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.836 Fit side-chains REVERT: A 344 GLN cc_start: 0.8818 (mt0) cc_final: 0.8102 (mm-40) REVERT: B 344 GLN cc_start: 0.8682 (mt0) cc_final: 0.7725 (tp-100) REVERT: C 344 GLN cc_start: 0.8615 (mt0) cc_final: 0.7607 (tp-100) REVERT: D 344 GLN cc_start: 0.8725 (mt0) cc_final: 0.7675 (tp-100) REVERT: E 97 TYR cc_start: 0.8297 (t80) cc_final: 0.8005 (t80) REVERT: E 344 GLN cc_start: 0.8705 (mt0) cc_final: 0.7719 (tp-100) outliers start: 8 outliers final: 6 residues processed: 226 average time/residue: 1.4551 time to fit residues: 360.7998 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 : 1.876 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.132629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105920 restraints weight = 40555.995| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.80 r_work: 0.2761 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16000 Z= 0.250 Angle : 0.630 8.280 21825 Z= 0.334 Chirality : 0.046 0.165 2385 Planarity : 0.005 0.042 2740 Dihedral : 4.981 43.256 2098 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % 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: 1.05 (0.18), residues: 1890 helix: 1.22 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.17 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 309 HIS 0.006 0.002 HIS A 326 PHE 0.029 0.002 PHE B 248 TYR 0.035 0.002 TYR A 97 ARG 0.003 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.06634 ( 970) hydrogen bonds : angle 4.77573 ( 2840) covalent geometry : bond 0.00588 (16000) covalent geometry : angle 0.62986 (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 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 1.862 Fit side-chains REVERT: A 344 GLN cc_start: 0.8881 (mt0) cc_final: 0.8186 (mm-40) REVERT: B 344 GLN cc_start: 0.8761 (mt0) cc_final: 0.7885 (tp-100) REVERT: C 344 GLN cc_start: 0.8736 (mt0) cc_final: 0.7746 (tp-100) REVERT: D 344 GLN cc_start: 0.8828 (mt0) cc_final: 0.7847 (tp-100) REVERT: E 344 GLN cc_start: 0.8831 (mt0) cc_final: 0.7845 (tp-100) outliers start: 8 outliers final: 6 residues processed: 226 average time/residue: 1.4705 time to fit residues: 363.7296 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 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 = 0.3462 r_free = 0.3462 target = 0.135363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106401 restraints weight = 41218.303| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.07 r_work: 0.2845 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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= 0.168 Angle : 0.552 8.074 21825 Z= 0.292 Chirality : 0.040 0.157 2385 Planarity : 0.005 0.040 2740 Dihedral : 4.801 43.563 2098 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % 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: 1.31 (0.18), residues: 1890 helix: 1.43 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.023 0.002 PHE C 248 TYR 0.032 0.002 TYR D 97 ARG 0.003 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 970) hydrogen bonds : angle 4.66795 ( 2840) covalent geometry : bond 0.00378 (16000) covalent geometry : angle 0.55151 (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 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 1.691 Fit side-chains REVERT: A 344 GLN cc_start: 0.8826 (mt0) cc_final: 0.8028 (mm-40) REVERT: B 344 GLN cc_start: 0.8751 (mt0) cc_final: 0.7694 (tp-100) REVERT: C 344 GLN cc_start: 0.8671 (mt0) cc_final: 0.7529 (tp-100) REVERT: D 344 GLN cc_start: 0.8778 (mt0) cc_final: 0.7679 (tp-100) REVERT: E 344 GLN cc_start: 0.8778 (mt0) cc_final: 0.7620 (tp-100) REVERT: E 356 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6538 (mtt90) outliers start: 8 outliers final: 7 residues processed: 223 average time/residue: 1.4800 time to fit residues: 360.2223 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 : 1.681 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 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 = 0.3462 r_free = 0.3462 target = 0.135454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106364 restraints weight = 33814.214| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.05 r_work: 0.2865 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 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 = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1374 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= 0.169 Angle : 0.553 8.478 21825 Z= 0.292 Chirality : 0.041 0.157 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.775 43.370 2098 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.42 % Allowed : 10.33 % 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: 1.32 (0.18), residues: 1890 helix: 1.43 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.023 0.002 PHE E 248 TYR 0.032 0.002 TYR A 97 ARG 0.003 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 970) hydrogen bonds : angle 4.65207 ( 2840) covalent geometry : bond 0.00381 (16000) covalent geometry : angle 0.55298 (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 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 1.768 Fit side-chains REVERT: A 344 GLN cc_start: 0.8870 (mt0) cc_final: 0.8154 (mm-40) REVERT: B 344 GLN cc_start: 0.8760 (mt0) cc_final: 0.7793 (tp-100) REVERT: C 344 GLN cc_start: 0.8724 (mt0) cc_final: 0.7665 (tp-100) REVERT: D 344 GLN cc_start: 0.8814 (mt0) cc_final: 0.7796 (tp-100) REVERT: E 344 GLN cc_start: 0.8822 (mt0) cc_final: 0.7747 (tp-100) outliers start: 7 outliers final: 7 residues processed: 223 average time/residue: 1.5059 time to fit residues: 366.9400 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107831 restraints weight = 38446.958| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.67 r_work: 0.2884 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1339 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 : 0.529 8.807 21825 Z= 0.279 Chirality : 0.039 0.156 2385 Planarity : 0.004 0.038 2740 Dihedral : 4.684 43.934 2098 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.48 % Allowed : 10.51 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 1890 helix: 1.50 (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 0.017 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.021 0.002 PHE C 248 TYR 0.029 0.001 TYR A 97 ARG 0.003 0.000 ARG C 356 Details of bonding type rmsd hydrogen bonds : bond 0.05497 ( 970) hydrogen bonds : angle 4.60476 ( 2840) covalent geometry : bond 0.00320 (16000) covalent geometry : angle 0.52917 (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 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.954 Fit side-chains REVERT: A 344 GLN cc_start: 0.8821 (mt0) cc_final: 0.8065 (mm-40) REVERT: B 344 GLN cc_start: 0.8723 (mt0) cc_final: 0.7706 (tp-100) REVERT: C 344 GLN cc_start: 0.8641 (mt0) cc_final: 0.7569 (tp-100) REVERT: D 344 GLN cc_start: 0.8752 (mt0) cc_final: 0.7690 (tp-100) REVERT: E 344 GLN cc_start: 0.8775 (mt0) cc_final: 0.7680 (tp-100) REVERT: E 356 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6560 (mtt90) outliers start: 8 outliers final: 7 residues processed: 226 average time/residue: 1.5145 time to fit residues: 374.9611 Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 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 = 0.3467 r_free = 0.3467 target = 0.135810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106938 restraints weight = 34262.502| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.12 r_work: 0.2890 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1390 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= 0.168 Angle : 0.553 9.033 21825 Z= 0.292 Chirality : 0.041 0.157 2385 Planarity : 0.005 0.039 2740 Dihedral : 4.743 43.136 2098 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.48 % Allowed : 10.57 % 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: 1.36 (0.18), residues: 1890 helix: 1.46 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 309 HIS 0.004 0.001 HIS A 326 PHE 0.022 0.002 PHE E 248 TYR 0.032 0.002 TYR A 97 ARG 0.003 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.05779 ( 970) hydrogen bonds : angle 4.63575 ( 2840) covalent geometry : bond 0.00379 (16000) covalent geometry : angle 0.55326 (21825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13835.72 seconds wall clock time: 241 minutes 31.04 seconds (14491.04 seconds total)