Starting phenix.real_space_refine on Mon Dec 30 04:33:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a0e_15052/12_2024/8a0e_15052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a0e_15052/12_2024/8a0e_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_15052/12_2024/8a0e_15052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a0e_15052/12_2024/8a0e_15052.map" model { file = "/net/cci-nas-00/data/ceres_data/8a0e_15052/12_2024/8a0e_15052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a0e_15052/12_2024/8a0e_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-5532/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: 11.42, per 1000 atoms: 0.95 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: 3.04 Conformation dependent library (CDL) restraints added in 2.6 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: 1.41 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: 3.55 Time building geometry restraints manager: 3.40 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: 1.250 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.350 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:16.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- 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 12334 Z= 0.221 Angle : 0.598 13.671 16741 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 *********************** 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 : 1.363 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: 1.8030 time to fit residues: 281.6202 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 : 1.425 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 12334 Z= 0.219 Angle : 0.562 13.144 16741 Z= 0.289 Chirality : 0.044 0.158 1881 Planarity : 0.005 0.047 2151 Dihedral : 9.851 76.721 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 *********************** 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 : 1.349 Fit side-chains revert: symmetry clash REVERT: B 251 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7589 (mptt) REVERT: C 86 ASP cc_start: 0.7930 (m-30) cc_final: 0.7641 (m-30) REVERT: C 192 MET cc_start: 0.7312 (ttm) cc_final: 0.7111 (ttt) REVERT: C 363 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5816 (mpm) REVERT: D 189 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6976 (mm-40) REVERT: D 251 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (mtmt) REVERT: E 141 MET cc_start: 0.5024 (ptm) cc_final: 0.4627 (pmt) outliers start: 9 outliers final: 2 residues processed: 134 average time/residue: 1.9284 time to fit residues: 274.9887 Evaluate side-chains 125 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN C 122 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12334 Z= 0.190 Angle : 0.520 11.668 16741 Z= 0.268 Chirality : 0.043 0.156 1881 Planarity : 0.004 0.048 2151 Dihedral : 8.475 68.888 1885 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.02 % Allowed : 6.80 % 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: 0.14 (0.21), residues: 1507 helix: 0.48 (0.21), residues: 641 sheet: 2.02 (0.40), residues: 179 loop : -0.77 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 327 HIS 0.007 0.001 HIS B 289 PHE 0.015 0.001 PHE C 355 TYR 0.014 0.001 TYR C 221 ARG 0.004 0.000 ARG C 91 *********************** 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 135 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.454 Fit side-chains REVERT: A 114 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: B 251 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7576 (mptt) REVERT: C 86 ASP cc_start: 0.7901 (m-30) cc_final: 0.7627 (m-30) REVERT: D 251 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8323 (mtmt) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 1.9163 time to fit residues: 254.4983 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 : 1.524 ------------------------------------------------------------------------------- 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 274 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 363 MET 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 135 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12334 Z= 0.133 Angle : 0.472 11.811 16741 Z= 0.242 Chirality : 0.041 0.144 1881 Planarity : 0.004 0.049 2151 Dihedral : 7.535 61.830 1885 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.40 % 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: 0.37 (0.21), residues: 1507 helix: 0.74 (0.21), residues: 640 sheet: 2.04 (0.40), residues: 180 loop : -0.69 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.011 0.001 PHE C 355 TYR 0.011 0.001 TYR C 221 ARG 0.005 0.000 ARG B 331 *********************** 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 137 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.454 Fit side-chains REVERT: A 114 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: C 71 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: C 86 ASP cc_start: 0.7905 (m-30) cc_final: 0.7612 (m-30) outliers start: 12 outliers final: 6 residues processed: 131 average time/residue: 1.7679 time to fit residues: 246.7772 Evaluate side-chains 123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 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 363 MET Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12334 Z= 0.233 Angle : 0.531 11.595 16741 Z= 0.274 Chirality : 0.043 0.161 1881 Planarity : 0.004 0.047 2151 Dihedral : 7.633 58.573 1885 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.94 % Allowed : 8.76 % Favored : 90.30 % 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: 0.31 (0.21), residues: 1507 helix: 0.72 (0.21), residues: 642 sheet: 2.01 (0.40), residues: 179 loop : -0.77 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.006 0.001 HIS B 289 PHE 0.015 0.001 PHE C 355 TYR 0.017 0.001 TYR C 221 ARG 0.006 0.000 ARG B 331 *********************** 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 129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.397 Fit side-chains REVERT: A 32 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7514 (ttm110) REVERT: A 114 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: A 150 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 71 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 86 ASP cc_start: 0.7905 (m-30) cc_final: 0.7661 (m-30) outliers start: 12 outliers final: 6 residues processed: 124 average time/residue: 1.7676 time to fit residues: 233.8051 Evaluate side-chains 124 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 285 VAL Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 146 optimal weight: 0.0470 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12334 Z= 0.252 Angle : 0.552 8.219 16741 Z= 0.286 Chirality : 0.044 0.166 1881 Planarity : 0.004 0.047 2151 Dihedral : 7.731 62.264 1885 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.17 % Allowed : 8.60 % Favored : 90.23 % 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: 0.24 (0.21), residues: 1507 helix: 0.68 (0.21), residues: 643 sheet: 1.96 (0.40), residues: 179 loop : -0.82 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 327 HIS 0.007 0.001 HIS B 289 PHE 0.019 0.001 PHE C 355 TYR 0.016 0.002 TYR C 221 ARG 0.006 0.000 ARG B 331 *********************** 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 131 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.421 Fit side-chains REVERT: A 32 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7537 (ttm110) REVERT: A 114 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: A 150 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 157 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: C 71 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 86 ASP cc_start: 0.7905 (m-30) cc_final: 0.7628 (m-30) REVERT: D 251 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8337 (mtmt) outliers start: 15 outliers final: 5 residues processed: 123 average time/residue: 1.7952 time to fit residues: 235.3841 Evaluate side-chains 123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 B residue 157 GLU 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 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.0030 chunk 67 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12334 Z= 0.125 Angle : 0.477 10.631 16741 Z= 0.244 Chirality : 0.041 0.143 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.353 59.930 1885 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.78 % Allowed : 9.30 % Favored : 89.91 % 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: 0.44 (0.21), residues: 1507 helix: 0.90 (0.21), residues: 640 sheet: 1.97 (0.41), residues: 174 loop : -0.71 (0.22), residues: 693 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 0.010 0.001 PHE C 355 TYR 0.010 0.001 TYR C 221 ARG 0.006 0.000 ARG B 331 *********************** 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 127 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.344 Fit side-chains REVERT: A 32 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7498 (ttm110) REVERT: A 114 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: C 71 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: C 86 ASP cc_start: 0.7918 (m-30) cc_final: 0.7671 (m-30) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 1.7812 time to fit residues: 233.7826 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 : 1.394 ------------------------------------------------------------------------------- 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 C residue 71 GLU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12334 Z= 0.269 Angle : 0.558 10.054 16741 Z= 0.288 Chirality : 0.044 0.169 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.526 62.406 1885 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.02 % Allowed : 9.23 % Favored : 89.76 % 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: 0.30 (0.21), residues: 1507 helix: 0.79 (0.21), residues: 644 sheet: 1.90 (0.40), residues: 174 loop : -0.80 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.006 0.002 HIS B 289 PHE 0.017 0.002 PHE C 355 TYR 0.018 0.002 TYR C 221 ARG 0.006 0.000 ARG B 331 *********************** 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 131 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: A 150 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: B 157 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: C 71 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: C 86 ASP cc_start: 0.7932 (m-30) cc_final: 0.7676 (m-30) outliers start: 13 outliers final: 7 residues processed: 124 average time/residue: 1.8712 time to fit residues: 246.5591 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 : 1.259 ------------------------------------------------------------------------------- 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 B residue 157 GLU 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 174 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 0.0970 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN E 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12334 Z= 0.112 Angle : 0.482 10.550 16741 Z= 0.247 Chirality : 0.041 0.144 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.281 60.620 1885 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.86 % Allowed : 9.77 % Favored : 89.37 % 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: 0.50 (0.21), residues: 1507 helix: 0.98 (0.21), residues: 641 sheet: 1.99 (0.41), residues: 174 loop : -0.71 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 327 HIS 0.004 0.001 HIS B 289 PHE 0.009 0.001 PHE C 355 TYR 0.011 0.001 TYR C 221 ARG 0.010 0.000 ARG C 91 *********************** 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: 11 poor density : 117 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: A 150 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: B 157 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: C 71 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 86 ASP cc_start: 0.7917 (m-30) cc_final: 0.7671 (m-30) REVERT: C 363 MET cc_start: 0.6352 (mmm) cc_final: 0.6107 (mpm) outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 1.8928 time to fit residues: 252.9757 Evaluate side-chains 122 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 B residue 157 GLU 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 359 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 chunk 138 optimal weight: 0.2980 chunk 119 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN E 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12334 Z= 0.129 Angle : 0.473 11.011 16741 Z= 0.242 Chirality : 0.041 0.142 1881 Planarity : 0.004 0.044 2151 Dihedral : 7.034 58.732 1885 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.63 % Allowed : 10.01 % Favored : 89.37 % 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: 0.56 (0.21), residues: 1507 helix: 1.02 (0.21), residues: 644 sheet: 2.04 (0.41), residues: 174 loop : -0.68 (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 0.012 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 ********************** 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 124 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: A 181 ASP cc_start: 0.8061 (m-30) cc_final: 0.7858 (m-30) REVERT: B 157 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: C 71 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 86 ASP cc_start: 0.7910 (m-30) cc_final: 0.7686 (m-30) REVERT: C 363 MET cc_start: 0.6393 (mmm) cc_final: 0.6131 (mpm) outliers start: 8 outliers final: 4 residues processed: 122 average time/residue: 1.8084 time to fit residues: 235.1050 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 : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 157 GLU 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 359 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.0010 chunk 105 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 E 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095807 restraints weight = 21070.967| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.12 r_work: 0.2951 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12334 Z= 0.128 Angle : 0.475 10.980 16741 Z= 0.242 Chirality : 0.041 0.142 1881 Planarity : 0.004 0.044 2151 Dihedral : 6.898 56.685 1885 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.70 % Allowed : 9.77 % Favored : 89.52 % 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: 0.61 (0.21), residues: 1507 helix: 1.06 (0.21), residues: 644 sheet: 2.05 (0.40), residues: 180 loop : -0.67 (0.22), residues: 683 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 0.009 0.001 PHE C 355 TYR 0.011 0.001 TYR A 221 ARG 0.009 0.000 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.85 seconds wall clock time: 81 minutes 38.72 seconds (4898.72 seconds total)