Starting phenix.real_space_refine on Wed Jul 30 09:16:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.map" model { file = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a0e_15052/07_2025/8a0e_15052.cif" } resolution = 2.8 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= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 70 5.16 5 C 7638 2.51 5 N 2069 2.21 5 O 2297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12082 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2770 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 356, 2767 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 16, 'TRANS': 339} Conformer: "B" Number of residues, atoms: 356, 2767 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 16, 'TRANS': 339} bond proxies already assigned to first conformer: 2820 Chain: "B" Number of atoms: 2736 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Conformer: "C" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 bond proxies already assigned to first conformer: 2785 Chain: "C" Number of atoms: 2724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 350, 2720 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 350, 2720 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2771 Chain: "D" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2597 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1049 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N ALA A 11 " occ=0.83 ... (3 atoms not shown) pdb=" CB ALA A 11 " occ=0.83 residue: pdb=" N LEU A 14 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 14 " occ=0.88 residue: pdb=" N ALA A 15 " occ=0.94 ... (3 atoms not shown) pdb=" CB ALA A 15 " occ=0.94 residue: pdb=" N HIS A 20 " occ=0.95 ... (8 atoms not shown) pdb=" NE2 HIS A 20 " occ=0.95 residue: pdb=" N PRO A 26 " occ=0.91 ... (5 atoms not shown) pdb=" CD PRO A 26 " occ=0.91 residue: pdb=" N ALA B 11 " occ=0.82 ... (3 atoms not shown) pdb=" CB ALA B 11 " occ=0.82 residue: pdb=" N LEU B 14 " occ=0.82 ... (6 atoms not shown) pdb=" CD2 LEU B 14 " occ=0.82 residue: pdb=" N ALA B 15 " occ=0.90 ... (3 atoms not shown) pdb=" CB ALA B 15 " occ=0.90 residue: pdb=" N HIS B 20 " occ=0.91 ... (8 atoms not shown) pdb=" NE2 HIS B 20 " occ=0.91 residue: pdb=" N ALA C 11 " occ=0.83 ... (3 atoms not shown) pdb=" CB ALA C 11 " occ=0.83 residue: pdb=" N LEU C 14 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU C 14 " occ=0.88 residue: pdb=" N ALA C 15 " occ=0.94 ... (3 atoms not shown) pdb=" CB ALA C 15 " occ=0.94 ... (remaining 6 not shown) Time building chain proxies: 12.35, per 1000 atoms: 1.02 Number of scatterers: 12082 At special positions: 0 Unit cell: (92.02, 96.32, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 8 15.00 O 2297 8.00 N 2069 7.00 C 7638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 73 " distance=2.04 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: 3.95 Conformation dependent library (CDL) restraints added in 2.9 seconds 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 12 sheets defined 50.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.693A pdb=" N ALA A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 removed outlier: 3.613A pdb=" N ARG A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 55 through 74 Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.973A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.848A pdb=" N VAL A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 173 through 197 removed outlier: 3.700A pdb=" N PHE A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 181 " --> pdb=" O CYS A 177 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.501A pdb=" N ASN A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.773A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.577A pdb=" N TRP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.790A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.839A pdb=" N HIS A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.968A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 327' Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.504A pdb=" N VAL A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Proline residue: A 348 - end of helix removed outlier: 3.605A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.523A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.957A pdb=" N ARG B 38 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.572A pdb=" N GLY B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 74 removed outlier: 3.681A pdb=" N THR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.781A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 removed outlier: 4.064A pdb=" N ASP B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.654A pdb=" N ASN B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 196 removed outlier: 3.635A pdb=" N PHE B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 180 " --> pdb=" O TYR B 176 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.551A pdb=" N MET B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 removed outlier: 3.903A pdb=" N ASN B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.682A pdb=" N TRP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.648A pdb=" N LEU B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.703A pdb=" N HIS B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.304A pdb=" N ALA B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.549A pdb=" N VAL B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) Proline residue: B 348 - end of helix removed outlier: 3.551A pdb=" N GLU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.750A pdb=" N MET B 363 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.814A pdb=" N ARG C 38 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 removed outlier: 3.510A pdb=" N GLU C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 74 removed outlier: 3.993A pdb=" N ASN C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 89 removed outlier: 3.739A pdb=" N THR C 88 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 removed outlier: 3.511A pdb=" N ARG C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 removed outlier: 3.553A pdb=" N VAL C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.619A pdb=" N LEU C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 197 removed outlier: 3.521A pdb=" N GLU C 180 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 181 " --> pdb=" O CSS C 177 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 3.657A pdb=" N GLN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.885A pdb=" N ASN C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 removed outlier: 3.733A pdb=" N TRP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 259 through 272 removed outlier: 3.587A pdb=" N PHE C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.832A pdb=" N HIS C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.865A pdb=" N ALA C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 320 through 327' Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.608A pdb=" N VAL C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.518A pdb=" N ARG D 38 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 49 through 52 Processing helix chain 'D' and resid 53 through 74 removed outlier: 3.711A pdb=" N THR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 112 through 122 removed outlier: 3.967A pdb=" N TYR D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 141 removed outlier: 3.616A pdb=" N GLU D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.668A pdb=" N LEU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 197 removed outlier: 3.528A pdb=" N LYS D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 180 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 181 " --> pdb=" O CSS D 177 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 202 through 215 removed outlier: 4.093A pdb=" N ASN D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.687A pdb=" N TRP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 249 removed outlier: 3.508A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 removed outlier: 3.696A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.652A pdb=" N HIS D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.037A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 325 " --> pdb=" O PRO D 321 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 327' Processing helix chain 'D' and resid 342 through 355 Proline residue: D 348 - end of helix Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.873A pdb=" N MET D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP D 360 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 361 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 4.207A pdb=" N GLU E 124 " --> pdb=" O GLY E 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 232 removed outlier: 6.821A pdb=" N LEU A 128 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 98 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 279 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 100 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 281 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 102 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 302 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.524A pdb=" N TYR A 147 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 232 removed outlier: 6.744A pdb=" N LEU B 128 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR B 98 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE B 279 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 100 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU B 281 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 102 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR B 302 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 232 removed outlier: 6.897A pdb=" N LEU C 128 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 302 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AA7, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.831A pdb=" N LEU D 128 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 302 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA D 303 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL D 339 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR D 305 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 21 Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 32 removed outlier: 6.811A pdb=" N VAL E 59 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET E 43 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS E 57 " --> pdb=" O MET E 43 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR E 45 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS E 55 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.572A pdb=" N ASN E 87 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 138 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 145 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.572A pdb=" N ASN E 87 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 150 " --> pdb=" O LEU E 134 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1290 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: 5.83 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 4991 1.40 - 1.58: 7209 1.58 - 1.75: 16 1.75 - 1.93: 116 1.93 - 2.11: 2 Bond restraints: 12334 Sorted by residual: bond pdb=" CB CSS D 177 " pdb=" SG CSS D 177 " ideal model delta sigma weight residual 1.823 1.755 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB CSS C 177 " pdb=" SG CSS C 177 " ideal model delta sigma weight residual 1.823 1.756 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O3 NAD D 402 " pdb=" PA NAD D 402 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.31e+00 bond pdb=" O3 NAD A 401 " pdb=" PA NAD A 401 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" O3 NAD C 401 " pdb=" PA NAD C 401 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 12329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 16597 2.73 - 5.47: 135 5.47 - 8.20: 6 8.20 - 10.94: 2 10.94 - 13.67: 1 Bond angle restraints: 16741 Sorted by residual: angle pdb=" CA CYS A 177 " pdb=" C CYS A 177 " pdb=" O CYS A 177 " ideal model delta sigma weight residual 119.60 123.92 -4.32 1.17e+00 7.31e-01 1.36e+01 angle pdb=" PA NAD A 401 " pdb=" O3 NAD A 401 " pdb=" PN NAD A 401 " ideal model delta sigma weight residual 126.50 136.85 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N CYS A 177 " pdb=" CA CYS A 177 " pdb=" C CYS A 177 " ideal model delta sigma weight residual 112.90 108.56 4.34 1.31e+00 5.83e-01 1.10e+01 angle pdb=" PA NAD B 401 " pdb=" O3 NAD B 401 " pdb=" PN NAD B 401 " ideal model delta sigma weight residual 126.50 134.95 -8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" PA NAD C 401 " pdb=" O3 NAD C 401 " pdb=" PN NAD C 401 " ideal model delta sigma weight residual 126.50 134.07 -7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 16736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 6922 18.16 - 36.31: 443 36.31 - 54.47: 90 54.47 - 72.63: 27 72.63 - 90.79: 32 Dihedral angle restraints: 7514 sinusoidal: 3119 harmonic: 4395 Sorted by residual: dihedral pdb=" CA CYS E 73 " pdb=" C CYS E 73 " pdb=" N PRO E 74 " pdb=" CA PRO E 74 " ideal model delta harmonic sigma weight residual 180.00 147.50 32.50 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 73 " pdb=" CB CYS E 73 " ideal model delta sinusoidal sigma weight residual -86.00 -136.15 50.15 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA GLY A 53 " pdb=" C GLY A 53 " pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1447 0.047 - 0.095: 323 0.095 - 0.142: 105 0.142 - 0.190: 1 0.190 - 0.237: 5 Chirality restraints: 1881 Sorted by residual: chirality pdb=" C1D NAD C 401 " pdb=" C2D NAD C 401 " pdb=" N1N NAD C 401 " pdb=" O4D NAD C 401 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1D NAD A 401 " pdb=" C2D NAD A 401 " pdb=" N1N NAD A 401 " pdb=" O4D NAD A 401 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C1D NAD B 401 " pdb=" C2D NAD B 401 " pdb=" N1N NAD B 401 " pdb=" O4D NAD B 401 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1878 not shown) Planarity restraints: 2151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 402 " 0.034 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" C2N NAD D 402 " -0.052 2.00e-02 2.50e+03 pdb=" C3N NAD D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C4N NAD D 402 " 0.012 2.00e-02 2.50e+03 pdb=" C5N NAD D 402 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C7N NAD D 402 " 0.024 2.00e-02 2.50e+03 pdb=" N1N NAD D 402 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 36 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 37 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 37 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 37 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 202 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 203 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " 0.023 5.00e-02 4.00e+02 ... (remaining 2148 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 374 2.72 - 3.27: 11459 3.27 - 3.81: 18027 3.81 - 4.36: 24580 4.36 - 4.90: 41298 Nonbonded interactions: 95738 Sorted by model distance: nonbonded pdb=" OG SER C 105 " pdb=" OG1 THR C 131 " model vdw 2.176 3.040 nonbonded pdb=" OG SER A 315 " pdb=" O1A NAD B 401 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 105 " pdb=" OG1 THR A 131 " model vdw 2.225 3.040 nonbonded pdb=" O GLU A 323 " pdb=" OG SER A 326 " model vdw 2.238 3.040 nonbonded pdb=" OG SER D 105 " pdb=" OG1 THR D 131 " model vdw 2.245 3.040 ... (remaining 95733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 79 or resid 84 through 104 or resid 106 through \ 176 or resid 178 through 239 or resid 241 through 285 or resid 287 through 363) \ ) selection = (chain 'B' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) selection = (chain 'C' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) selection = (chain 'D' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) } 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=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.100 Set scattering table: 0.130 Process input model: 42.510 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:31.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.003 0.068 12335 Z= 0.168 Angle : 0.598 13.671 16743 Z= 0.298 Chirality : 0.044 0.237 1881 Planarity : 0.004 0.051 2151 Dihedral : 14.458 90.785 4691 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.22 (0.22), residues: 1507 helix: -0.14 (0.21), residues: 611 sheet: 2.00 (0.40), residues: 185 loop : -0.66 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.008 0.001 HIS B 289 PHE 0.014 0.001 PHE C 355 TYR 0.013 0.001 TYR B 221 ARG 0.003 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.22708 ( 459) hydrogen bonds : angle 6.85438 ( 1290) SS BOND : bond 0.00584 ( 1) SS BOND : angle 1.90397 ( 2) covalent geometry : bond 0.00346 (12334) covalent geometry : angle 0.59752 (16741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.352 Fit side-chains REVERT: A 359 MET cc_start: 0.7538 (tpt) cc_final: 0.7328 (tpt) REVERT: B 251 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7679 (mptt) REVERT: B 252 ASN cc_start: 0.8136 (m-40) cc_final: 0.7888 (m-40) REVERT: C 86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7344 (p0) REVERT: E 141 MET cc_start: 0.4947 (ptm) cc_final: 0.4626 (pmt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.9228 time to fit residues: 300.4646 Evaluate side-chains 114 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 298 ASN D 252 ASN E 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.092032 restraints weight = 27146.436| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.42 r_work: 0.2912 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12335 Z= 0.147 Angle : 0.562 13.144 16743 Z= 0.289 Chirality : 0.044 0.158 1881 Planarity : 0.005 0.047 2151 Dihedral : 9.851 76.722 1885 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.70 % Allowed : 6.18 % Favored : 93.12 % 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: -0.01 (0.21), residues: 1507 helix: 0.22 (0.21), residues: 636 sheet: 1.99 (0.41), residues: 179 loop : -0.70 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.008 0.002 HIS B 289 PHE 0.019 0.001 PHE C 355 TYR 0.015 0.002 TYR C 221 ARG 0.004 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05931 ( 459) hydrogen bonds : angle 4.78043 ( 1290) SS BOND : bond 0.00380 ( 1) SS BOND : angle 1.34366 ( 2) covalent geometry : bond 0.00339 (12334) covalent geometry : angle 0.56153 (16741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 18 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6257 (mp) REVERT: B 251 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7881 (mptt) REVERT: B 252 ASN cc_start: 0.8616 (m-40) cc_final: 0.8362 (m110) REVERT: C 86 ASP cc_start: 0.8008 (m-30) cc_final: 0.7710 (m-30) REVERT: C 192 MET cc_start: 0.8247 (ttm) cc_final: 0.8002 (ttt) REVERT: C 359 MET cc_start: 0.8083 (tpt) cc_final: 0.7842 (tpt) REVERT: C 363 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5821 (mpm) REVERT: D 174 GLU cc_start: 0.7314 (tp30) cc_final: 0.7113 (tp30) REVERT: D 189 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7236 (mm-40) REVERT: D 251 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8546 (mtmt) REVERT: E 141 MET cc_start: 0.5043 (ptm) cc_final: 0.4662 (pmt) outliers start: 9 outliers final: 2 residues processed: 134 average time/residue: 1.7943 time to fit residues: 255.4049 Evaluate side-chains 127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.0070 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 19 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091058 restraints weight = 22735.746| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.21 r_work: 0.2887 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12335 Z= 0.157 Angle : 0.553 11.873 16743 Z= 0.287 Chirality : 0.044 0.163 1881 Planarity : 0.005 0.048 2151 Dihedral : 8.485 66.398 1885 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.33 % Allowed : 6.49 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.05 (0.21), residues: 1507 helix: 0.42 (0.21), residues: 640 sheet: 1.95 (0.40), residues: 179 loop : -0.83 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 327 HIS 0.008 0.002 HIS D 289 PHE 0.020 0.001 PHE C 355 TYR 0.016 0.002 TYR C 221 ARG 0.005 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 459) hydrogen bonds : angle 4.48473 ( 1290) SS BOND : bond 0.00546 ( 1) SS BOND : angle 2.15113 ( 2) covalent geometry : bond 0.00372 (12334) covalent geometry : angle 0.55280 (16741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.271 Fit side-chains REVERT: A 114 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: B 157 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: B 251 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7843 (mptt) REVERT: C 71 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: C 86 ASP cc_start: 0.7983 (m-30) cc_final: 0.7714 (m-30) REVERT: C 192 MET cc_start: 0.8053 (ttm) cc_final: 0.7831 (ttp) REVERT: C 359 MET cc_start: 0.8097 (tpt) cc_final: 0.7891 (tpt) REVERT: C 363 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5900 (mpm) REVERT: D 174 GLU cc_start: 0.7289 (tp30) cc_final: 0.7008 (tp30) REVERT: D 251 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8543 (mtmt) outliers start: 17 outliers final: 7 residues processed: 125 average time/residue: 1.9617 time to fit residues: 259.9315 Evaluate side-chains 129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 33 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 147 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.087963 restraints weight = 26160.889| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.36 r_work: 0.2855 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12335 Z= 0.245 Angle : 0.648 11.835 16743 Z= 0.336 Chirality : 0.048 0.185 1881 Planarity : 0.005 0.050 2151 Dihedral : 8.451 67.242 1885 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.95 % Allowed : 7.43 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.21 (0.21), residues: 1507 helix: 0.28 (0.21), residues: 642 sheet: 1.76 (0.39), residues: 186 loop : -1.07 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 327 HIS 0.009 0.002 HIS B 289 PHE 0.025 0.002 PHE C 355 TYR 0.020 0.002 TYR C 221 ARG 0.004 0.001 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.07638 ( 459) hydrogen bonds : angle 4.63591 ( 1290) SS BOND : bond 0.00833 ( 1) SS BOND : angle 2.24102 ( 2) covalent geometry : bond 0.00606 (12334) covalent geometry : angle 0.64769 (16741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.504 Fit side-chains REVERT: A 32 ARG cc_start: 0.8482 (tpp-160) cc_final: 0.8227 (ttm110) REVERT: A 114 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: A 150 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: B 157 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 251 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7957 (mptt) REVERT: C 71 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 86 ASP cc_start: 0.8017 (m-30) cc_final: 0.7760 (m-30) REVERT: C 192 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7882 (ttp) REVERT: C 363 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5902 (mpm) REVERT: D 174 GLU cc_start: 0.7384 (tp30) cc_final: 0.7073 (tp30) REVERT: D 251 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8558 (mtmt) outliers start: 25 outliers final: 10 residues processed: 127 average time/residue: 1.8538 time to fit residues: 250.4902 Evaluate side-chains 131 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089693 restraints weight = 21757.395| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.15 r_work: 0.2867 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12335 Z= 0.202 Angle : 0.592 10.742 16743 Z= 0.309 Chirality : 0.046 0.175 1881 Planarity : 0.005 0.050 2151 Dihedral : 8.227 68.029 1885 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.64 % Allowed : 8.37 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.17 (0.21), residues: 1507 helix: 0.36 (0.21), residues: 642 sheet: 1.78 (0.39), residues: 186 loop : -1.10 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 327 HIS 0.008 0.002 HIS B 289 PHE 0.022 0.002 PHE C 355 TYR 0.017 0.002 TYR C 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.06707 ( 459) hydrogen bonds : angle 4.48080 ( 1290) SS BOND : bond 0.00664 ( 1) SS BOND : angle 1.63520 ( 2) covalent geometry : bond 0.00492 (12334) covalent geometry : angle 0.59185 (16741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.966 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.8193 (ttm110) REVERT: A 114 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: A 150 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: B 157 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 71 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: C 86 ASP cc_start: 0.8006 (m-30) cc_final: 0.7745 (m-30) REVERT: D 174 GLU cc_start: 0.7341 (tp30) cc_final: 0.7031 (tp30) REVERT: D 251 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8556 (mtmt) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 2.4268 time to fit residues: 325.2419 Evaluate side-chains 128 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 23 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089327 restraints weight = 29507.940| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.71 r_work: 0.2833 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12335 Z= 0.175 Angle : 0.568 8.660 16743 Z= 0.297 Chirality : 0.044 0.169 1881 Planarity : 0.005 0.049 2151 Dihedral : 8.078 67.723 1885 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.88 % Allowed : 8.44 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.10 (0.21), residues: 1507 helix: 0.46 (0.21), residues: 642 sheet: 1.71 (0.39), residues: 181 loop : -1.06 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 327 HIS 0.007 0.001 HIS B 289 PHE 0.018 0.002 PHE C 355 TYR 0.016 0.002 TYR C 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.06198 ( 459) hydrogen bonds : angle 4.40148 ( 1290) SS BOND : bond 0.00623 ( 1) SS BOND : angle 3.57252 ( 2) covalent geometry : bond 0.00423 (12334) covalent geometry : angle 0.56710 (16741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8437 (tpp-160) cc_final: 0.8206 (ttm110) REVERT: A 114 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: A 150 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: B 91 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6876 (mtm180) REVERT: B 157 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 71 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 86 ASP cc_start: 0.7932 (m-30) cc_final: 0.7651 (m-30) REVERT: D 174 GLU cc_start: 0.7352 (tp30) cc_final: 0.7031 (tp30) REVERT: D 189 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7564 (mm-40) REVERT: D 251 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8531 (mtmt) outliers start: 24 outliers final: 10 residues processed: 129 average time/residue: 2.1261 time to fit residues: 290.8746 Evaluate side-chains 127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 6 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093911 restraints weight = 25444.041| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.36 r_work: 0.2901 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12335 Z= 0.091 Angle : 0.471 8.405 16743 Z= 0.244 Chirality : 0.041 0.143 1881 Planarity : 0.004 0.047 2151 Dihedral : 7.589 64.501 1885 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.78 % Allowed : 9.93 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1507 helix: 0.74 (0.21), residues: 642 sheet: 1.73 (0.40), residues: 175 loop : -0.85 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.009 0.001 PHE C 355 TYR 0.009 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 459) hydrogen bonds : angle 4.02918 ( 1290) SS BOND : bond 0.00580 ( 1) SS BOND : angle 2.86529 ( 2) covalent geometry : bond 0.00194 (12334) covalent geometry : angle 0.46997 (16741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.308 Fit side-chains REVERT: A 32 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8143 (ttm110) REVERT: A 114 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: A 359 MET cc_start: 0.7661 (tpt) cc_final: 0.7346 (tpt) REVERT: C 86 ASP cc_start: 0.7940 (m-30) cc_final: 0.7694 (m-30) REVERT: D 174 GLU cc_start: 0.7209 (tp30) cc_final: 0.6917 (tp30) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 1.7690 time to fit residues: 233.5885 Evaluate side-chains 122 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 363 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 114 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092902 restraints weight = 22019.129| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.16 r_work: 0.2909 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12335 Z= 0.115 Angle : 0.495 9.231 16743 Z= 0.257 Chirality : 0.042 0.153 1881 Planarity : 0.004 0.046 2151 Dihedral : 7.499 63.312 1885 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.86 % Allowed : 9.93 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.29 (0.21), residues: 1507 helix: 0.80 (0.21), residues: 643 sheet: 1.87 (0.41), residues: 174 loop : -0.82 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.011 0.001 PHE C 355 TYR 0.014 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 459) hydrogen bonds : angle 4.05766 ( 1290) SS BOND : bond 0.00593 ( 1) SS BOND : angle 2.65280 ( 2) covalent geometry : bond 0.00263 (12334) covalent geometry : angle 0.49383 (16741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.8140 (ttm110) REVERT: A 114 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: C 86 ASP cc_start: 0.7958 (m-30) cc_final: 0.7697 (m-30) REVERT: D 174 GLU cc_start: 0.7254 (tp30) cc_final: 0.6950 (tp30) outliers start: 11 outliers final: 6 residues processed: 123 average time/residue: 1.8338 time to fit residues: 240.4557 Evaluate side-chains 123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 363 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095609 restraints weight = 28195.988| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.58 r_work: 0.2932 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12335 Z= 0.085 Angle : 0.455 9.846 16743 Z= 0.235 Chirality : 0.041 0.141 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.219 60.006 1885 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.63 % Allowed : 10.16 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.47 (0.21), residues: 1507 helix: 0.97 (0.21), residues: 640 sheet: 1.71 (0.40), residues: 186 loop : -0.70 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 327 HIS 0.004 0.001 HIS B 289 PHE 0.007 0.001 PHE C 355 TYR 0.009 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 459) hydrogen bonds : angle 3.86631 ( 1290) SS BOND : bond 0.00606 ( 1) SS BOND : angle 2.32587 ( 2) covalent geometry : bond 0.00177 (12334) covalent geometry : angle 0.45394 (16741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.8170 (ttm110) REVERT: A 114 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: C 86 ASP cc_start: 0.7950 (m-30) cc_final: 0.7678 (m-30) REVERT: D 174 GLU cc_start: 0.7235 (tp30) cc_final: 0.6935 (tp30) outliers start: 8 outliers final: 5 residues processed: 125 average time/residue: 1.8055 time to fit residues: 240.2872 Evaluate side-chains 122 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 359 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN D 122 HIS E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.094517 restraints weight = 28063.735| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.58 r_work: 0.2925 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12335 Z= 0.089 Angle : 0.463 10.310 16743 Z= 0.237 Chirality : 0.041 0.142 1881 Planarity : 0.004 0.044 2151 Dihedral : 7.038 59.299 1885 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.70 % Allowed : 10.32 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.58 (0.21), residues: 1507 helix: 1.04 (0.21), residues: 644 sheet: 1.98 (0.41), residues: 174 loop : -0.65 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.004 0.001 HIS B 289 PHE 0.008 0.001 PHE C 355 TYR 0.011 0.001 TYR A 221 ARG 0.010 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 459) hydrogen bonds : angle 3.82971 ( 1290) SS BOND : bond 0.00549 ( 1) SS BOND : angle 2.28483 ( 2) covalent geometry : bond 0.00192 (12334) covalent geometry : angle 0.46237 (16741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8138 (ttm110) REVERT: A 114 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: A 150 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: A 359 MET cc_start: 0.7564 (tpt) cc_final: 0.7200 (tpt) REVERT: C 86 ASP cc_start: 0.7903 (m-30) cc_final: 0.7676 (m-30) REVERT: D 174 GLU cc_start: 0.7216 (tp30) cc_final: 0.6887 (tp30) outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 1.7382 time to fit residues: 231.2241 Evaluate side-chains 121 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 359 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 130 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 122 HIS E 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.094247 restraints weight = 25087.879| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.45 r_work: 0.2916 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12335 Z= 0.098 Angle : 0.467 10.447 16743 Z= 0.241 Chirality : 0.041 0.145 1881 Planarity : 0.004 0.044 2151 Dihedral : 7.013 57.435 1885 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.78 % Allowed : 10.48 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.58 (0.21), residues: 1507 helix: 1.04 (0.21), residues: 645 sheet: 1.95 (0.40), residues: 180 loop : -0.66 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.004 0.001 HIS B 289 PHE 0.010 0.001 PHE C 355 TYR 0.012 0.001 TYR A 221 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 459) hydrogen bonds : angle 3.85701 ( 1290) SS BOND : bond 0.00561 ( 1) SS BOND : angle 2.28327 ( 2) covalent geometry : bond 0.00217 (12334) covalent geometry : angle 0.46666 (16741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11007.84 seconds wall clock time: 195 minutes 5.27 seconds (11705.27 seconds total)