Starting phenix.real_space_refine on Wed Feb 14 04:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/02_2024/8g59_29736_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.088 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 S 58 5.16 5 C 5503 2.51 5 N 1444 2.21 5 O 1577 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8583 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2509 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "Y" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 365 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1739 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1739 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2231 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2220 Unusual residues: {'YN9': 1} Classifications: {'peptide': 281, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 269, None: 1} Not linked: pdbres="THR R 324 " pdbres="YN9 R 401 " Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 282, 2220 Unusual residues: {'YN9': 1} Classifications: {'peptide': 281, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 269, None: 1} Not linked: pdbres="THR R 324 " pdbres="YN9 R 401 " Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2260 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE R 115 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE R 115 " occ=0.50 Time building chain proxies: 5.98, per 1000 atoms: 0.70 Number of scatterers: 8583 At special positions: 0 Unit cell: (105.456, 121.68, 115.596, 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 58 16.00 F 1 9.00 O 1577 8.00 N 1444 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 34.2% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.655A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 56 through 58 No H-bonds generated for 'chain 'Y' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.737A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.983A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.636A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'R' and resid 43 through 69 Processing helix chain 'R' and resid 78 through 100 removed outlier: 3.956A pdb=" N ALA R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 110 through 141 removed outlier: 4.695A pdb=" N APHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 175 removed outlier: 3.561A pdb=" N ALA R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 171 " --> pdb=" O ALA R 167 " (cutoff:3.500A) Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 201 through 244 removed outlier: 3.556A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Proline residue: R 219 - end of helix removed outlier: 3.958A pdb=" N ARG R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 291 removed outlier: 3.614A pdb=" N LEU R 262 " --> pdb=" O GLN R 258 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 300 through 320 removed outlier: 3.903A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.846A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.983A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.484A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.700A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.531A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.541A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.527A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS S 22 " --> pdb=" O LEU S 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.572A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.559A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.656A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.624A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.408A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 177 through 182 383 hydrogen bonds defined for protein. 1114 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: 2.76 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1365 1.26 - 1.40: 2177 1.40 - 1.53: 4857 1.53 - 1.67: 280 1.67 - 1.81: 84 Bond restraints: 8763 Sorted by residual: bond pdb=" C PHE R 260 " pdb=" O PHE R 260 " ideal model delta sigma weight residual 1.233 1.117 0.116 1.46e-02 4.69e+03 6.29e+01 bond pdb=" N GLN R 258 " pdb=" CA GLN R 258 " ideal model delta sigma weight residual 1.458 1.383 0.074 1.33e-02 5.65e+03 3.12e+01 bond pdb=" N ASP R 259 " pdb=" CA ASP R 259 " ideal model delta sigma weight residual 1.456 1.393 0.063 1.18e-02 7.18e+03 2.84e+01 bond pdb=" C ARG R 36 " pdb=" O ARG R 36 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.25e-02 6.40e+03 2.54e+01 bond pdb=" CA ASP A 346 " pdb=" C ASP A 346 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.26e-02 6.30e+03 2.20e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 206 107.00 - 113.77: 4920 113.77 - 120.53: 3309 120.53 - 127.30: 3385 127.30 - 134.06: 90 Bond angle restraints: 11910 Sorted by residual: angle pdb=" N PHE R 260 " pdb=" CA PHE R 260 " pdb=" C PHE R 260 " ideal model delta sigma weight residual 114.04 102.67 11.37 1.24e+00 6.50e-01 8.41e+01 angle pdb=" C ALA R 91 " pdb=" N ILE R 92 " pdb=" CA ILE R 92 " ideal model delta sigma weight residual 120.24 124.87 -4.63 6.30e-01 2.52e+00 5.39e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 110.62 117.17 -6.55 1.02e+00 9.61e-01 4.13e+01 angle pdb=" N LEU A 358 " pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 111.36 118.33 -6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" C ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta sigma weight residual 110.94 120.06 -9.12 1.65e+00 3.67e-01 3.05e+01 ... (remaining 11905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4693 15.94 - 31.87: 361 31.87 - 47.81: 63 47.81 - 63.75: 14 63.75 - 79.68: 8 Dihedral angle restraints: 5139 sinusoidal: 1895 harmonic: 3244 Sorted by residual: dihedral pdb=" C ASP R 259 " pdb=" N ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta harmonic sigma weight residual -122.60 -144.58 21.98 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" N ASP R 259 " pdb=" C ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta harmonic sigma weight residual 122.80 142.49 -19.69 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 27.64 65.36 1 1.00e+01 1.00e-02 5.60e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1389 0.197 - 0.394: 3 0.394 - 0.591: 0 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASP R 259 " pdb=" N ASP R 259 " pdb=" C ASP R 259 " pdb=" CB ASP R 259 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA ARG R 254 " pdb=" N ARG R 254 " pdb=" C ARG R 254 " pdb=" CB ARG R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA GLN R 258 " pdb=" N GLN R 258 " pdb=" C GLN R 258 " pdb=" CB GLN R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1390 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 257 " -0.028 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C GLN R 257 " 0.098 2.00e-02 2.50e+03 pdb=" O GLN R 257 " -0.037 2.00e-02 2.50e+03 pdb=" N GLN R 258 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO S 75 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 299 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO R 300 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 300 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 300 " 0.034 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 56 2.52 - 3.12: 6344 3.12 - 3.71: 13332 3.71 - 4.31: 19324 4.31 - 4.90: 32229 Nonbonded interactions: 71285 Sorted by model distance: nonbonded pdb=" NH2 ARG R 238 " pdb=" OD2 ASP R 259 " model vdw 1.930 2.520 nonbonded pdb=" O CYS R 60 " pdb=" CD2 LEU R 64 " model vdw 1.953 3.460 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.183 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.222 2.440 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.255 2.520 ... (remaining 71280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 1.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.005 0.116 8763 Z= 0.337 Angle : 0.759 16.011 11910 Z= 0.436 Chirality : 0.053 0.985 1393 Planarity : 0.006 0.112 1491 Dihedral : 12.177 79.684 3031 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1095 helix: 0.23 (0.25), residues: 387 sheet: 0.39 (0.30), residues: 301 loop : -0.65 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 63 HIS 0.004 0.001 HIS R 251 PHE 0.016 0.001 PHE R 311 TYR 0.017 0.001 TYR A 302 ARG 0.007 0.000 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 209 LYS cc_start: 0.9253 (mttm) cc_final: 0.9006 (mttp) REVERT: S 223 ASP cc_start: 0.8111 (m-30) cc_final: 0.7514 (m-30) REVERT: R 165 TYR cc_start: 0.7006 (t80) cc_final: 0.6179 (t80) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 1.5117 time to fit residues: 255.7425 Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 259 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.0000 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 186 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8763 Z= 0.169 Angle : 0.582 10.668 11910 Z= 0.295 Chirality : 0.042 0.133 1393 Planarity : 0.005 0.075 1491 Dihedral : 5.281 65.620 1203 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.10 % Allowed : 10.02 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1095 helix: 1.08 (0.27), residues: 377 sheet: 0.55 (0.31), residues: 299 loop : -0.48 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.017 0.001 PHE R 263 TYR 0.010 0.001 TYR A 302 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.891 Fit side-chains REVERT: B 61 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7680 (ppp) REVERT: B 335 PHE cc_start: 0.8668 (m-80) cc_final: 0.8431 (m-80) REVERT: A 193 ASP cc_start: 0.7879 (p0) cc_final: 0.7658 (p0) REVERT: R 165 TYR cc_start: 0.6991 (t80) cc_final: 0.5916 (t80) REVERT: R 240 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5584 (ptt90) outliers start: 10 outliers final: 4 residues processed: 147 average time/residue: 1.4742 time to fit residues: 228.2508 Evaluate side-chains 128 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN A 188 HIS ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8763 Z= 0.174 Angle : 0.550 10.434 11910 Z= 0.278 Chirality : 0.041 0.133 1393 Planarity : 0.004 0.063 1491 Dihedral : 4.501 54.925 1201 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.65 % Allowed : 12.33 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1095 helix: 1.40 (0.27), residues: 371 sheet: 0.62 (0.31), residues: 299 loop : -0.38 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.010 0.001 PHE R 304 TYR 0.008 0.001 TYR S 190 ARG 0.012 0.001 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.408 Fit side-chains REVERT: A 240 MET cc_start: 0.6711 (ptt) cc_final: 0.6378 (ptp) REVERT: A 346 ASP cc_start: 0.5784 (m-30) cc_final: 0.4999 (t70) REVERT: R 165 TYR cc_start: 0.7024 (t80) cc_final: 0.5924 (t80) outliers start: 15 outliers final: 5 residues processed: 140 average time/residue: 1.5528 time to fit residues: 229.7385 Evaluate side-chains 141 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 333 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN Y 59 ASN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8763 Z= 0.177 Angle : 0.541 10.979 11910 Z= 0.273 Chirality : 0.041 0.138 1393 Planarity : 0.004 0.058 1491 Dihedral : 4.418 52.522 1201 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.43 % Allowed : 13.99 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1095 helix: 1.33 (0.27), residues: 380 sheet: 0.74 (0.31), residues: 292 loop : -0.33 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE R 263 TYR 0.008 0.001 TYR S 190 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7946 (p0) cc_final: 0.7694 (p0) REVERT: A 240 MET cc_start: 0.6618 (ptt) cc_final: 0.6305 (ptp) REVERT: R 165 TYR cc_start: 0.7072 (t80) cc_final: 0.5952 (t80) outliers start: 13 outliers final: 6 residues processed: 147 average time/residue: 1.4558 time to fit residues: 225.6462 Evaluate side-chains 137 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 272 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 chunk 26 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8763 Z= 0.430 Angle : 0.682 11.766 11910 Z= 0.348 Chirality : 0.047 0.176 1393 Planarity : 0.005 0.063 1491 Dihedral : 5.118 56.333 1201 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.09 % Allowed : 15.42 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1095 helix: 0.68 (0.27), residues: 382 sheet: 0.64 (0.30), residues: 292 loop : -0.38 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 104 HIS 0.006 0.002 HIS B 142 PHE 0.019 0.002 PHE R 260 TYR 0.014 0.002 TYR Y 40 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7499 (mtp85) REVERT: B 78 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8147 (mptm) REVERT: A 240 MET cc_start: 0.6676 (ptt) cc_final: 0.6422 (ptp) REVERT: A 346 ASP cc_start: 0.6044 (m-30) cc_final: 0.4935 (t70) REVERT: R 165 TYR cc_start: 0.7302 (t80) cc_final: 0.7097 (t80) REVERT: R 178 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6897 (mmp80) outliers start: 19 outliers final: 8 residues processed: 147 average time/residue: 1.5050 time to fit residues: 232.5408 Evaluate side-chains 153 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 178 ARG Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN A 204 GLN R 252 GLN R 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8763 Z= 0.200 Angle : 0.558 8.723 11910 Z= 0.287 Chirality : 0.042 0.147 1393 Planarity : 0.005 0.058 1491 Dihedral : 4.667 53.962 1201 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.43 % Allowed : 17.40 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1095 helix: 1.14 (0.27), residues: 377 sheet: 0.64 (0.30), residues: 303 loop : -0.29 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE R 260 TYR 0.008 0.001 TYR S 190 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: S 223 ASP cc_start: 0.7966 (m-30) cc_final: 0.7567 (m-30) REVERT: A 240 MET cc_start: 0.6678 (ptt) cc_final: 0.6463 (ptp) REVERT: R 165 TYR cc_start: 0.7183 (t80) cc_final: 0.5984 (t80) REVERT: R 240 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6339 (ptp90) outliers start: 13 outliers final: 2 residues processed: 155 average time/residue: 1.5620 time to fit residues: 255.2979 Evaluate side-chains 142 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8763 Z= 0.282 Angle : 0.604 10.862 11910 Z= 0.309 Chirality : 0.043 0.154 1393 Planarity : 0.005 0.060 1491 Dihedral : 4.825 58.127 1201 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.87 % Allowed : 18.17 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1095 helix: 1.11 (0.27), residues: 379 sheet: 0.67 (0.30), residues: 303 loop : -0.38 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 104 HIS 0.007 0.001 HIS A 188 PHE 0.014 0.002 PHE R 260 TYR 0.009 0.001 TYR S 103 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7479 (mtp85) REVERT: B 78 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8061 (mptm) REVERT: S 202 ARG cc_start: 0.6818 (ptt180) cc_final: 0.6606 (ptt90) REVERT: R 165 TYR cc_start: 0.7271 (t80) cc_final: 0.6643 (t80) REVERT: R 240 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6151 (ptp90) outliers start: 17 outliers final: 6 residues processed: 150 average time/residue: 1.4830 time to fit residues: 233.9741 Evaluate side-chains 149 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 268 ASN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8763 Z= 0.205 Angle : 0.582 8.779 11910 Z= 0.299 Chirality : 0.042 0.151 1393 Planarity : 0.005 0.057 1491 Dihedral : 4.737 60.202 1201 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.54 % Allowed : 18.94 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1095 helix: 1.26 (0.27), residues: 384 sheet: 0.68 (0.30), residues: 303 loop : -0.26 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS A 188 PHE 0.018 0.001 PHE R 263 TYR 0.009 0.001 TYR S 190 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: B 96 ARG cc_start: 0.6842 (mpp-170) cc_final: 0.6559 (mtm110) REVERT: B 228 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7427 (p0) REVERT: S 192 MET cc_start: 0.8707 (ttp) cc_final: 0.8493 (tmm) REVERT: S 223 ASP cc_start: 0.7904 (m-30) cc_final: 0.7468 (m-30) REVERT: A 247 MET cc_start: 0.8407 (mtm) cc_final: 0.8123 (mtt) REVERT: R 165 TYR cc_start: 0.7217 (t80) cc_final: 0.5999 (t80) REVERT: R 240 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6214 (ptp90) outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 1.5236 time to fit residues: 235.8579 Evaluate side-chains 137 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN B 268 ASN B 340 ASN Y 59 ASN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8763 Z= 0.183 Angle : 0.571 11.413 11910 Z= 0.292 Chirality : 0.041 0.146 1393 Planarity : 0.005 0.059 1491 Dihedral : 4.647 61.604 1201 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.87 % Allowed : 18.72 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1095 helix: 1.42 (0.27), residues: 384 sheet: 0.70 (0.30), residues: 294 loop : -0.20 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.001 PHE R 260 TYR 0.017 0.001 TYR A 302 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7404 (mtp85) REVERT: B 78 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8082 (mptm) REVERT: B 228 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7526 (p0) REVERT: S 192 MET cc_start: 0.8754 (ttp) cc_final: 0.8540 (ttp) REVERT: S 223 ASP cc_start: 0.8184 (m-30) cc_final: 0.7807 (m-30) REVERT: A 247 MET cc_start: 0.8389 (mtm) cc_final: 0.8121 (mtt) REVERT: R 165 TYR cc_start: 0.7187 (t80) cc_final: 0.5918 (t80) REVERT: R 240 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6134 (ptp90) outliers start: 17 outliers final: 6 residues processed: 149 average time/residue: 1.5895 time to fit residues: 249.1424 Evaluate side-chains 138 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 268 ASN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8763 Z= 0.262 Angle : 0.613 11.838 11910 Z= 0.313 Chirality : 0.043 0.157 1393 Planarity : 0.005 0.062 1491 Dihedral : 4.822 63.992 1201 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.21 % Allowed : 19.27 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1095 helix: 1.24 (0.27), residues: 389 sheet: 0.72 (0.30), residues: 309 loop : -0.29 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 104 HIS 0.006 0.001 HIS A 188 PHE 0.018 0.002 PHE R 263 TYR 0.012 0.001 TYR A 302 ARG 0.009 0.001 ARG R 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7400 (mtp85) REVERT: B 78 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8088 (mptm) REVERT: B 228 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7740 (p0) REVERT: S 192 MET cc_start: 0.8763 (ttp) cc_final: 0.8548 (ttp) REVERT: A 240 MET cc_start: 0.5693 (ptp) cc_final: 0.5135 (ttm) REVERT: A 247 MET cc_start: 0.8410 (mtm) cc_final: 0.8120 (mtt) REVERT: R 165 TYR cc_start: 0.7269 (t80) cc_final: 0.6070 (t80) REVERT: R 240 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6182 (ptp90) outliers start: 11 outliers final: 5 residues processed: 144 average time/residue: 1.5433 time to fit residues: 234.0806 Evaluate side-chains 137 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.153831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119187 restraints weight = 20563.737| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.44 r_work: 0.3508 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8763 Z= 0.331 Angle : 0.642 9.106 11910 Z= 0.329 Chirality : 0.045 0.162 1393 Planarity : 0.005 0.067 1491 Dihedral : 4.961 62.015 1201 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 18.39 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1095 helix: 1.09 (0.27), residues: 386 sheet: 0.68 (0.29), residues: 309 loop : -0.31 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 104 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.002 PHE R 177 TYR 0.016 0.002 TYR A 302 ARG 0.013 0.001 ARG R 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.14 seconds wall clock time: 78 minutes 12.22 seconds (4692.22 seconds total)