Starting phenix.real_space_refine on Fri Sep 11 15:29:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wkw_21811/09_2026/6wkw_21811.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 49 5.16 5 C 6287 2.51 5 N 1779 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10037 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 329, 2396 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 319} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 329, 2396 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 319} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 2425 Chain: "C" Number of atoms: 2502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2495 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 320} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 330, 2495 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 320} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 2527 Chain: "B" Number of atoms: 2463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2456 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 3, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 76 Conformer: "B" Number of residues, atoms: 330, 2456 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 3, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 76 bond proxies already assigned to first conformer: 2488 Chain: "A" Number of atoms: 2493 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2484 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 5, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 330, 2484 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 5, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 2516 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 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: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N HIS C 250 " occ=0.88 ... (8 atoms not shown) pdb=" NE2 HIS C 250 " occ=0.88 residue: pdb=" N TYR A 234 " occ=0.77 ... (10 atoms not shown) pdb=" OH TYR A 234 " occ=0.77 residue: pdb=" N AGLN A 328 " occ=0.55 ... (16 atoms not shown) pdb=" NE2BGLN A 328 " occ=0.45 Time building chain proxies: 3.94, per 1000 atoms: 0.39 Number of scatterers: 10037 At special positions: 0 Unit cell: (104.4, 94.83, 81.78, 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 49 16.00 P 8 15.00 O 1914 8.00 N 1779 7.00 C 6287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 585.2 milliseconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 36.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'D' and resid 46 through 51 removed outlier: 4.222A pdb=" N ILE D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 133 through 147 removed outlier: 3.596A pdb=" N HIS D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.796A pdb=" N ARG D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 3.744A pdb=" N GLN D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.598A pdb=" N LEU D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.501A pdb=" N MET D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 286 removed outlier: 4.623A pdb=" N GLN D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 removed outlier: 4.375A pdb=" N ARG D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.906A pdb=" N ILE C 68 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.744A pdb=" N LEU C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.535A pdb=" N ARG C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.718A pdb=" N GLN C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 removed outlier: 3.509A pdb=" N LEU C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.639A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.606A pdb=" N LEU C 275 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 276 " --> pdb=" O GLY C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 329 through 347 removed outlier: 3.836A pdb=" N GLU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 112 through 120 removed outlier: 4.209A pdb=" N GLU B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.958A pdb=" N ASP B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 164 through 172 removed outlier: 4.013A pdb=" N GLU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.760A pdb=" N ALA B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.839A pdb=" N GLN B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 4.732A pdb=" N ARG B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.892A pdb=" N LEU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.615A pdb=" N GLU A 67 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 68 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N HIS A 69 " --> pdb=" O GLN A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.218A pdb=" N ASN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.940A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.603A pdb=" N ALA A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 removed outlier: 3.598A pdb=" N GLN A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.583A pdb=" N ARG A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.536A pdb=" N GLN A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.115A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.716A pdb=" N LEU A 275 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 276 " --> pdb=" O GLY A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.836A pdb=" N GLU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.623A pdb=" N VAL D 36 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU D 35 " --> pdb=" O VAL D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AA3, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.671A pdb=" N VAL D 206 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 226 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE D 208 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR D 182 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER D 240 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY D 184 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 293 through 295 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 38 removed outlier: 6.106A pdb=" N VAL C 36 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.688A pdb=" N VAL C 206 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 removed outlier: 6.385A pdb=" N VAL C 239 " --> pdb=" O VAL C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.462A pdb=" N ALA C 293 " --> pdb=" O ILE C 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 removed outlier: 6.027A pdb=" N PHE B 208 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 183 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR B 209 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 185 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 239 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 293 through 295 Processing sheet with id=AB4, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.691A pdb=" N VAL A 36 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 78 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA A 79 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 225 removed outlier: 6.806A pdb=" N LEU A 185 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 293 through 295 249 hydrogen bonds defined for protein. 723 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: 1.16 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1716 1.29 - 1.42: 2560 1.42 - 1.55: 5842 1.55 - 1.67: 28 1.67 - 1.80: 76 Bond restraints: 10222 Sorted by residual: bond pdb=" C3B NAD C 401 " pdb=" C4B NAD C 401 " ideal model delta sigma weight residual 1.523 1.229 0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C3B NAD D 401 " pdb=" C4B NAD D 401 " ideal model delta sigma weight residual 1.523 1.231 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3B NAD B 401 " pdb=" C4B NAD B 401 " ideal model delta sigma weight residual 1.523 1.233 0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C3B NAD A 401 " pdb=" C4B NAD A 401 " ideal model delta sigma weight residual 1.523 1.234 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C1B NAD A 401 " pdb=" C2B NAD A 401 " ideal model delta sigma weight residual 1.534 1.268 0.266 2.00e-02 2.50e+03 1.76e+02 ... (remaining 10217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 13378 2.59 - 5.18: 473 5.18 - 7.76: 74 7.76 - 10.35: 14 10.35 - 12.94: 8 Bond angle restraints: 13947 Sorted by residual: angle pdb=" N VAL D 46 " pdb=" CA VAL D 46 " pdb=" C VAL D 46 " ideal model delta sigma weight residual 112.12 107.48 4.64 8.40e-01 1.42e+00 3.05e+01 angle pdb=" N VAL B 46 " pdb=" CA VAL B 46 " pdb=" C VAL B 46 " ideal model delta sigma weight residual 113.53 108.27 5.26 9.80e-01 1.04e+00 2.88e+01 angle pdb=" N ILE B 345 " pdb=" CA ILE B 345 " pdb=" C ILE B 345 " ideal model delta sigma weight residual 112.90 107.89 5.01 9.60e-01 1.09e+00 2.72e+01 angle pdb=" N GLY B 274 " pdb=" CA GLY B 274 " pdb=" C GLY B 274 " ideal model delta sigma weight residual 115.63 108.05 7.58 1.49e+00 4.50e-01 2.59e+01 angle pdb=" N LEU B 331 " pdb=" CA LEU B 331 " pdb=" C LEU B 331 " ideal model delta sigma weight residual 114.31 108.11 6.20 1.29e+00 6.01e-01 2.31e+01 ... (remaining 13942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5401 17.43 - 34.85: 496 34.85 - 52.28: 82 52.28 - 69.71: 17 69.71 - 87.14: 12 Dihedral angle restraints: 6008 sinusoidal: 2189 harmonic: 3819 Sorted by residual: dihedral pdb=" CA ILE A 349 " pdb=" C ILE A 349 " pdb=" N PRO A 350 " pdb=" CA PRO A 350 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA VAL B 77 " pdb=" C VAL B 77 " pdb=" N GLY B 78 " pdb=" CA GLY B 78 " ideal model delta harmonic sigma weight residual -180.00 -146.60 -33.40 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CA LEU C 38 " pdb=" C LEU C 38 " pdb=" N LEU C 39 " pdb=" CA LEU C 39 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1357 0.074 - 0.147: 262 0.147 - 0.221: 12 0.221 - 0.295: 6 0.295 - 0.369: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C3D NAD B 401 " pdb=" C2D NAD B 401 " pdb=" C4D NAD B 401 " pdb=" O3D NAD B 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3D NAD D 401 " pdb=" C2D NAD D 401 " pdb=" C4D NAD D 401 " pdb=" O3D NAD D 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3D NAD A 401 " pdb=" C2D NAD A 401 " pdb=" C4D NAD A 401 " pdb=" O3D NAD A 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1638 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 349 " 0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO A 350 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 188 " 0.026 2.00e-02 2.50e+03 2.37e-02 9.82e+00 pdb=" CG PHE C 188 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 188 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 188 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 188 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 188 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 188 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 357 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C VAL B 357 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL B 357 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 205 2.63 - 3.20: 9556 3.20 - 3.77: 15028 3.77 - 4.33: 21909 4.33 - 4.90: 36407 Nonbonded interactions: 83105 Sorted by model distance: nonbonded pdb=" OD2 ASP B 40 " pdb=" OG1 THR B 84 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASN B 246 " pdb=" ND2 ASN B 249 " model vdw 2.103 3.120 nonbonded pdb=" ND1 HIS A 251 " pdb=" OD1 ASP A 277 " model vdw 2.107 3.120 nonbonded pdb=" OE1 GLU B 132 " pdb=" NH2 ARG B 198 " model vdw 2.119 3.120 nonbonded pdb=" OD1 ASP A 296 " pdb=" OG1 THR A 319 " model vdw 2.143 3.040 ... (remaining 83100 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 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 43 or (resid 44 and (name N or name CA or name C or name \ O or name CB )) or resid 45 through 47 or (resid 48 and (name N or name CA or na \ me C or name O or name CB )) or resid 49 through 53 or (resid 54 through 56 and \ (name N or name CA or name C or name O or name CB )) or resid 57 through 62 or ( \ resid 63 through 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 68 or (resid 70 through 72 and (name N or name CA or name C or \ name O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C o \ r name O or name CB or name CG )) or (resid 75 through 76 and (name N or name CA \ or name C or name O or name CB )) or resid 77 through 91 or (resid 92 through 9 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 98 or (resid \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throug \ h 160 or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG )) or resid 162 through 163 or (resid 164 and (name N or name CA or name C \ or name O or name CB )) or resid 165 through 213 or (resid 214 and (name N or na \ me CA or name C or name O or name CB )) or resid 215 through 233 or (resid 234 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 235 \ through 246 or (resid 247 and (name N or name CA or name C or name O or name CB \ )) or resid 248 through 249 or resid 251 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 258 or (resid 2 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) or r \ esid 287 through 288 or (resid 289 and (name N or name CA or name C or name O or \ name CB )) or resid 290 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 292 through 306 or (resid 307 and (name N or name CA or \ name C or name O or name CB )) or resid 308 through 310 or (resid 311 through 3 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 314 through \ 327 or resid 329 through 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 336 through 341 or (resid 342 and (name \ N or name CA or name C or name O or name CB )) or resid 343 through 344 or (res \ id 345 through 346 and (name N or name CA or name C or name O or name CB )) or r \ esid 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 350 or (resid 351 and (name N or name CA or name C or name \ O or name CB )) or resid 352 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 358 or (resid 359 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 360 or (resi \ d 361 and (name N or name CA or name C or name O or name CB )) or resid 401)) selection = (chain 'B' and (resid 33 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 throu \ gh 56 and (name N or name CA or name C or name O or name CB )) or resid 57 throu \ gh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or r \ esid 67 through 68 or (resid 70 through 72 and (name N or name CA or name C or n \ ame O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 75 through 91 or (resid 92 through 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 158 through 160 or (resid 161 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 162 through 163 or (resid 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throu \ gh 206 or (resid 207 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2)) or resid 208 through 216 or (resid 217 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or resid 218 through \ 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) or r \ esid 225 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 through 246 or (resid 247 and (name N or name CA or nam \ e C or name O or name CB )) or resid 248 through 249 or resid 251 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 6 through 278 or (resid 279 through 280 and (name N or name CA or name C or name \ O or name CB )) or resid 281 through 285 or (resid 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 310 or (resid 311 through \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throug \ h 327 or resid 329 through 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 336 through 344 or (resid 345 through \ 346 and (name N or name CA or name C or name O or name CB )) or resid 347 throug \ h 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 353 or (resid 354 and (name N or name CA or name C or name O o \ r name CB )) or resid 355 through 360 or (resid 361 and (name N or name CA or na \ me C or name O or name CB )) or resid 401)) selection = (chain 'C' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 41 or (resid 42 and (name N or name CA or name C or name \ O or name CB )) or resid 43 or (resid 44 and (name N or name CA or name C or nam \ e O or name CB )) or resid 45 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 51 or (resid 52 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 53 or (resid 54 \ through 56 and (name N or name CA or name C or name O or name CB )) or resid 57 \ through 62 or (resid 63 through 64 and (name N or name CA or name C or name O or \ name CB )) or resid 65 or (resid 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 68 or (resid 70 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 or (resid 74 and (name N or na \ me CA or name C or name O or name CB or name CG )) or (resid 75 through 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 89 or (r \ esid 90 and (name N or name CA or name C or name O or name CB )) or resid 91 or \ (resid 92 through 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) \ or resid 100 through 113 or (resid 114 through 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 117 through 156 or (resid 157 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 158 through 206 \ or (resid 207 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 208 through 213 or (resid 214 and (name N or name CA or n \ ame C or name O or name CB )) or resid 215 through 216 or (resid 217 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 21 \ 8 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 229 or (resid 230 and (name N or name CA or name C or \ name O or name CB )) or resid 231 through 246 or (resid 247 and (name N or name \ CA or name C or name O or name CB )) or resid 248 through 249 or resid 251 throu \ gh 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 through 258 or (resid 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 285 or (resid 286 and (name N or name CA or n \ ame C or name O or name CB )) or resid 287 through 288 or (resid 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 326 or (resid \ 327 and (name N or name CA or name C or name O or name CB )) or resid 329 throu \ gh 334 or (resid 335 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 336 through 341 or (resid 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 344 or (resid 345 through 346 and \ (name N or name CA or name C or name O or name CB )) or resid 347 through 350 or \ (resid 351 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 2 through 358 or (resid 359 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 360 or (resid 361 and (name N or name CA or name C or n \ ame O or name CB )) or resid 401)) selection = (chain 'D' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 63 or (resid 64 and (name N or name CA or name C or name \ O or name CB )) or resid 65 through 68 or resid 70 through 93 or (resid 94 throu \ gh 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throu \ gh 156 or (resid 157 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 158 through 160 or (resid 161 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 162 through 163 or (resid 164 and ( \ name N or name CA or name C or name O or name CB )) or resid 165 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 218 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 229 or (resid 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 233 or (resid 23 \ 4 and (name N or name CA or name C or name O or name CB or name CG )) or resid 2 \ 35 through 249 or resid 251 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 288 or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 and (n \ ame N or name CA or name C or name O or name CB )) or resid 292 through 306 or ( \ resid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 \ through 327 or resid 329 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 401)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.130 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 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 : 0.017 0.294 10223 Z= 0.835 Angle : 1.193 12.940 13947 Z= 0.656 Chirality : 0.059 0.369 1641 Planarity : 0.005 0.097 1809 Dihedral : 14.386 87.135 3546 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.59 % Favored : 87.26 % Rotamer: Outliers : 0.52 % Allowed : 7.34 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.89 (0.17), residues: 1317 helix: -4.30 (0.13), residues: 474 sheet: -4.68 (0.29), residues: 159 loop : -3.41 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 272 TYR 0.024 0.002 TYR D 108 PHE 0.055 0.003 PHE C 188 TRP 0.006 0.002 TRP C 324 HIS 0.010 0.002 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.01736 / 0.84 (10222) covalent geometry : angle 1.19350 / 0.66 (13947) hydrogen bonds : bond 0.23103 / 15.92 ( 249) hydrogen bonds : angle 10.07842 / 6.82 ( 723) Misc. bond : bond 0.00083 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.408 Fit side-chains REVERT: C 48 MET cc_start: 0.8450 (tpp) cc_final: 0.8231 (tpt) REVERT: C 351 GLU cc_start: 0.7740 (pt0) cc_final: 0.7469 (pt0) REVERT: A 81 MET cc_start: 0.8800 (ptm) cc_final: 0.8573 (ptm) REVERT: A 351 GLU cc_start: 0.8096 (pm20) cc_final: 0.7818 (pm20) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1255 time to fit residues: 11.3979 Evaluate side-chains 47 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 149 ASN D 250 HIS A D 250 HIS B C 63 GLN C 149 ASN C 163 GLN C 250 HIS C 260 GLN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 244 ASN B 355 ASN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 83 HIS A 149 ASN A 242 HIS A 328 GLN B A 355 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083403 restraints weight = 48223.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087433 restraints weight = 27608.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.088267 restraints weight = 14751.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089572 restraints weight = 9905.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.090148 restraints weight = 8214.295| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10223 Z= 0.135 Angle : 0.635 10.398 13947 Z= 0.331 Chirality : 0.045 0.211 1641 Planarity : 0.005 0.077 1809 Dihedral : 6.121 42.632 1458 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 1.55 % Allowed : 9.62 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.19), residues: 1317 helix: -3.15 (0.18), residues: 472 sheet: -3.80 (0.31), residues: 180 loop : -2.97 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.019 0.001 TYR D 108 PHE 0.021 0.001 PHE C 188 TRP 0.010 0.002 TRP B 151 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (10222) covalent geometry : angle 0.63512 / 0.33 (13947) hydrogen bonds : bond 0.02804 / 1.89 ( 249) hydrogen bonds : angle 5.65272 / 3.83 ( 723) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.304 Fit side-chains REVERT: C 261 MET cc_start: 0.9012 (mtp) cc_final: 0.8789 (mtp) REVERT: C 351 GLU cc_start: 0.7678 (pt0) cc_final: 0.7391 (pt0) REVERT: B 48 MET cc_start: 0.7804 (tpp) cc_final: 0.7593 (tpt) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.0893 time to fit residues: 9.6800 Evaluate side-chains 58 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.078625 restraints weight = 59216.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081904 restraints weight = 39135.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.084976 restraints weight = 14449.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.085219 restraints weight = 9729.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.086690 restraints weight = 7285.401| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10223 Z= 0.263 Angle : 0.687 10.128 13947 Z= 0.355 Chirality : 0.048 0.225 1641 Planarity : 0.004 0.071 1809 Dihedral : 6.176 38.019 1458 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.61 % Favored : 90.24 % Rotamer: Outliers : 2.07 % Allowed : 12.20 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.20), residues: 1317 helix: -2.65 (0.20), residues: 474 sheet: -3.88 (0.32), residues: 171 loop : -2.60 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 103 TYR 0.021 0.002 TYR D 108 PHE 0.026 0.002 PHE C 188 TRP 0.007 0.001 TRP A 324 HIS 0.005 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (10222) covalent geometry : angle 0.68736 / 0.35 (13947) hydrogen bonds : bond 0.03211 / 2.17 ( 249) hydrogen bonds : angle 5.37410 / 3.64 ( 723) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.353 Fit side-chains REVERT: C 218 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: C 261 MET cc_start: 0.9025 (mtp) cc_final: 0.8796 (mtp) REVERT: C 351 GLU cc_start: 0.7585 (pt0) cc_final: 0.7331 (pt0) REVERT: A 351 GLU cc_start: 0.7819 (pm20) cc_final: 0.7485 (pm20) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.0798 time to fit residues: 7.3292 Evaluate side-chains 58 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084603 restraints weight = 52584.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088667 restraints weight = 33540.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090870 restraints weight = 13071.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091371 restraints weight = 9414.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092414 restraints weight = 7280.686| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10223 Z= 0.104 Angle : 0.577 10.830 13947 Z= 0.293 Chirality : 0.044 0.187 1641 Planarity : 0.004 0.056 1809 Dihedral : 5.474 35.835 1458 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 1.45 % Allowed : 13.65 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.21), residues: 1317 helix: -1.92 (0.22), residues: 463 sheet: -3.26 (0.31), residues: 217 loop : -2.29 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR D 108 PHE 0.021 0.001 PHE C 188 TRP 0.010 0.001 TRP C 324 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (10222) covalent geometry : angle 0.57665 / 0.29 (13947) hydrogen bonds : bond 0.02332 / 1.57 ( 249) hydrogen bonds : angle 4.66087 / 3.17 ( 723) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.348 Fit side-chains REVERT: C 261 MET cc_start: 0.8857 (mtp) cc_final: 0.8620 (mtp) REVERT: C 351 GLU cc_start: 0.7577 (pt0) cc_final: 0.7337 (pt0) REVERT: A 351 GLU cc_start: 0.7725 (pm20) cc_final: 0.7500 (pm20) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.0708 time to fit residues: 7.2574 Evaluate side-chains 56 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.0270 chunk 91 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083549 restraints weight = 50510.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087546 restraints weight = 29730.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088805 restraints weight = 13991.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.089814 restraints weight = 9685.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090632 restraints weight = 7824.524| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10223 Z= 0.117 Angle : 0.567 10.610 13947 Z= 0.288 Chirality : 0.043 0.181 1641 Planarity : 0.003 0.046 1809 Dihedral : 5.305 36.862 1458 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 1.86 % Allowed : 13.86 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.22), residues: 1317 helix: -1.49 (0.23), residues: 460 sheet: -3.08 (0.31), residues: 216 loop : -2.14 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.019 0.001 TYR D 108 PHE 0.014 0.001 PHE C 188 TRP 0.009 0.001 TRP C 324 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10222) covalent geometry : angle 0.56739 / 0.29 (13947) hydrogen bonds : bond 0.02350 / 1.61 ( 249) hydrogen bonds : angle 4.47132 / 3.04 ( 723) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.385 Fit side-chains REVERT: C 261 MET cc_start: 0.8842 (mtp) cc_final: 0.8615 (mtp) REVERT: C 351 GLU cc_start: 0.7602 (pt0) cc_final: 0.7360 (pt0) REVERT: A 152 LEU cc_start: 0.8875 (mt) cc_final: 0.8658 (mp) REVERT: A 348 ARG cc_start: 0.7299 (ptt-90) cc_final: 0.6879 (ptt180) REVERT: A 351 GLU cc_start: 0.7754 (pm20) cc_final: 0.6955 (pm20) outliers start: 13 outliers final: 7 residues processed: 66 average time/residue: 0.0803 time to fit residues: 8.3525 Evaluate side-chains 59 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 53 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.076808 restraints weight = 55883.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.081392 restraints weight = 34634.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.082853 restraints weight = 13043.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.083427 restraints weight = 9728.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.084799 restraints weight = 7641.924| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10223 Z= 0.228 Angle : 0.640 10.486 13947 Z= 0.327 Chirality : 0.047 0.196 1641 Planarity : 0.004 0.048 1809 Dihedral : 5.701 37.325 1458 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 2.17 % Allowed : 14.27 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.22), residues: 1317 helix: -1.38 (0.23), residues: 465 sheet: -3.11 (0.31), residues: 220 loop : -2.07 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.021 0.002 TYR A 325 PHE 0.015 0.002 PHE D 208 TRP 0.011 0.001 TRP C 324 HIS 0.004 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (10222) covalent geometry : angle 0.64016 / 0.33 (13947) hydrogen bonds : bond 0.02780 / 1.90 ( 249) hydrogen bonds : angle 4.80098 / 3.27 ( 723) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.288 Fit side-chains REVERT: C 218 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: C 261 MET cc_start: 0.9009 (mtp) cc_final: 0.8769 (mtp) REVERT: C 351 GLU cc_start: 0.7666 (pt0) cc_final: 0.7436 (pt0) REVERT: A 348 ARG cc_start: 0.7251 (ptt-90) cc_final: 0.6639 (ptt180) REVERT: A 351 GLU cc_start: 0.7803 (pm20) cc_final: 0.7137 (pm20) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.0849 time to fit residues: 7.8793 Evaluate side-chains 58 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 chunk 85 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.077727 restraints weight = 58478.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081804 restraints weight = 36599.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083996 restraints weight = 13628.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084376 restraints weight = 9991.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.085360 restraints weight = 7508.627| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10223 Z= 0.103 Angle : 0.570 12.553 13947 Z= 0.284 Chirality : 0.043 0.177 1641 Planarity : 0.003 0.040 1809 Dihedral : 5.222 37.486 1458 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 1.96 % Allowed : 14.99 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.22), residues: 1317 helix: -0.86 (0.24), residues: 460 sheet: -2.73 (0.35), residues: 181 loop : -1.96 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.018 0.001 TYR D 108 PHE 0.010 0.001 PHE D 303 TRP 0.009 0.001 TRP C 324 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (10222) covalent geometry : angle 0.57012 / 0.28 (13947) hydrogen bonds : bond 0.02187 / 1.46 ( 249) hydrogen bonds : angle 4.39337 / 3.00 ( 723) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.404 Fit side-chains REVERT: C 351 GLU cc_start: 0.7680 (pt0) cc_final: 0.7432 (pt0) REVERT: A 152 LEU cc_start: 0.8903 (mt) cc_final: 0.8672 (mp) REVERT: A 348 ARG cc_start: 0.7116 (ptt-90) cc_final: 0.6714 (ptt180) REVERT: A 351 GLU cc_start: 0.7678 (pm20) cc_final: 0.7215 (pm20) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.0844 time to fit residues: 8.7832 Evaluate side-chains 61 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080433 restraints weight = 59412.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.085337 restraints weight = 34594.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086796 restraints weight = 12532.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.087578 restraints weight = 9137.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088827 restraints weight = 7128.658| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10223 Z= 0.125 Angle : 0.570 10.874 13947 Z= 0.289 Chirality : 0.044 0.185 1641 Planarity : 0.003 0.038 1809 Dihedral : 5.189 38.440 1458 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 1.96 % Allowed : 14.79 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.23), residues: 1317 helix: -0.59 (0.25), residues: 466 sheet: -2.66 (0.35), residues: 180 loop : -1.92 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.020 0.001 TYR D 325 PHE 0.011 0.001 PHE C 188 TRP 0.011 0.001 TRP A 324 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10222) covalent geometry : angle 0.57045 / 0.29 (13947) hydrogen bonds : bond 0.02327 / 1.56 ( 249) hydrogen bonds : angle 4.35580 / 2.98 ( 723) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.382 Fit side-chains REVERT: C 218 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: C 351 GLU cc_start: 0.7630 (pt0) cc_final: 0.7393 (pt0) REVERT: A 152 LEU cc_start: 0.8953 (mt) cc_final: 0.8717 (mp) REVERT: A 348 ARG cc_start: 0.7048 (ptt-90) cc_final: 0.6688 (ptt180) REVERT: A 351 GLU cc_start: 0.7724 (pm20) cc_final: 0.7523 (pt0) outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.0942 time to fit residues: 9.2546 Evaluate side-chains 63 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 0.0470 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.077786 restraints weight = 57839.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.082377 restraints weight = 32729.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083109 restraints weight = 12788.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085845 restraints weight = 9380.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.086192 restraints weight = 6206.692| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10223 Z= 0.183 Angle : 0.620 12.632 13947 Z= 0.312 Chirality : 0.046 0.180 1641 Planarity : 0.004 0.037 1809 Dihedral : 5.438 38.649 1458 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 1.96 % Allowed : 14.79 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.23), residues: 1317 helix: -0.60 (0.24), residues: 472 sheet: -2.72 (0.35), residues: 181 loop : -1.89 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.023 0.002 TYR D 325 PHE 0.013 0.001 PHE D 208 TRP 0.006 0.001 TRP A 324 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (10222) covalent geometry : angle 0.62035 / 0.31 (13947) hydrogen bonds : bond 0.02526 / 1.71 ( 249) hydrogen bonds : angle 4.52510 / 3.09 ( 723) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.384 Fit side-chains REVERT: C 218 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: C 351 GLU cc_start: 0.7625 (pt0) cc_final: 0.7408 (pt0) REVERT: A 348 ARG cc_start: 0.6956 (ptt-90) cc_final: 0.6530 (ptt180) REVERT: A 351 GLU cc_start: 0.7786 (pm20) cc_final: 0.7514 (pt0) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.0886 time to fit residues: 8.2988 Evaluate side-chains 58 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.078948 restraints weight = 47994.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.082400 restraints weight = 23399.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083516 restraints weight = 13366.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.084235 restraints weight = 8962.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.084720 restraints weight = 8350.905| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10223 Z= 0.143 Angle : 0.587 13.285 13947 Z= 0.296 Chirality : 0.045 0.199 1641 Planarity : 0.003 0.038 1809 Dihedral : 5.313 39.085 1458 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 1.76 % Allowed : 15.20 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1317 helix: -0.40 (0.25), residues: 472 sheet: -2.65 (0.35), residues: 181 loop : -1.85 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.020 0.001 TYR D 325 PHE 0.012 0.001 PHE C 188 TRP 0.008 0.001 TRP C 324 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10222) covalent geometry : angle 0.58725 / 0.30 (13947) hydrogen bonds : bond 0.02345 / 1.59 ( 249) hydrogen bonds : angle 4.40812 / 3.00 ( 723) Misc. bond : bond 0.00037 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.385 Fit side-chains REVERT: C 218 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: C 351 GLU cc_start: 0.7691 (pt0) cc_final: 0.7473 (pt0) REVERT: A 152 LEU cc_start: 0.8988 (mt) cc_final: 0.8725 (mp) REVERT: A 348 ARG cc_start: 0.7011 (ptt-90) cc_final: 0.6752 (ptt180) REVERT: A 351 GLU cc_start: 0.7835 (pm20) cc_final: 0.7490 (pm20) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.0819 time to fit residues: 7.5479 Evaluate side-chains 59 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.0020 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.0060 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.079437 restraints weight = 49207.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.082819 restraints weight = 25771.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083966 restraints weight = 13391.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085161 restraints weight = 9262.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.085547 restraints weight = 7636.726| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10223 Z= 0.137 Angle : 0.593 14.163 13947 Z= 0.295 Chirality : 0.044 0.170 1641 Planarity : 0.003 0.038 1809 Dihedral : 5.275 40.226 1458 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 1.65 % Allowed : 15.31 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.23), residues: 1317 helix: -0.27 (0.25), residues: 472 sheet: -2.62 (0.35), residues: 181 loop : -1.80 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.022 0.002 TYR B 82 PHE 0.012 0.001 PHE C 188 TRP 0.008 0.001 TRP A 324 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10222) covalent geometry : angle 0.59341 / 0.30 (13947) hydrogen bonds : bond 0.02332 / 1.59 ( 249) hydrogen bonds : angle 4.34654 / 2.95 ( 723) Misc. bond : bond 0.00029 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1417.89 seconds wall clock time: 25 minutes 20.35 seconds (1520.35 seconds total)