Starting phenix.real_space_refine on Fri Sep 11 07:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xau_33099/09_2026/7xau_33099.cif" } resolution = 2.97 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= 0.002 sd= 0.101 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5351 2.51 5 N 1437 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 8443 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1923 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 12, 'TYR:plan': 1, 'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 178 Chain: "B" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1598 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.83, per 1000 atoms: 0.22 Number of scatterers: 8443 At special positions: 0 Unit cell: (87.74, 123.05, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1601 8.00 N 1437 7.00 C 5351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DTR F 4 " - " PHE F 3 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 353.6 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 1 " pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.648A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.880A pdb=" N ILE A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.820A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.874A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.824A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.548A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.969A pdb=" N TYR A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 4.036A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.582A pdb=" N ILE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.131A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.620A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.625A pdb=" N SER A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.606A pdb=" N ASN A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.841A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Proline residue: A 309 - end of helix removed outlier: 3.514A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.710A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.615A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.637A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.651A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.910A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.906A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 5.173A pdb=" N CYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.133A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.525A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.768A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.558A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 removed outlier: 4.129A pdb=" N ARG A 184 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.138A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.622A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.048A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.025A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.650A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.645A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.514A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.507A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.704A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.431A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 190 286 hydrogen bonds defined for protein. 792 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: 1.35 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2336 1.33 - 1.46: 2330 1.46 - 1.59: 3865 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 8605 Sorted by residual: bond pdb=" CA GLU C 138 " pdb=" CB GLU C 138 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.34e-02 5.57e+03 2.48e+01 bond pdb=" C LEU A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CG LEU C 95 " pdb=" CD1 LEU C 95 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" C THR C 243 " pdb=" N GLY C 244 " ideal model delta sigma weight residual 1.332 1.319 0.013 5.00e-03 4.00e+04 6.57e+00 bond pdb=" C CYS C 148 " pdb=" N CYS C 149 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.39e-02 5.18e+03 6.41e+00 ... (remaining 8600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11296 2.66 - 5.32: 361 5.32 - 7.98: 50 7.98 - 10.64: 6 10.64 - 13.29: 4 Bond angle restraints: 11717 Sorted by residual: angle pdb=" N LYS A 73 " pdb=" CA LYS A 73 " pdb=" C LYS A 73 " ideal model delta sigma weight residual 111.71 104.67 7.04 1.34e+00 5.57e-01 2.76e+01 angle pdb=" N MET B 243 " pdb=" CA MET B 243 " pdb=" C MET B 243 " ideal model delta sigma weight residual 113.41 107.18 6.23 1.22e+00 6.72e-01 2.60e+01 angle pdb=" N ALA A 72 " pdb=" CA ALA A 72 " pdb=" C ALA A 72 " ideal model delta sigma weight residual 110.53 116.64 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 106.21 111.16 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" C GLN A 187 " pdb=" N TRP A 188 " pdb=" CA TRP A 188 " ideal model delta sigma weight residual 122.46 128.81 -6.35 1.41e+00 5.03e-01 2.03e+01 ... (remaining 11712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4561 17.69 - 35.38: 427 35.38 - 53.07: 68 53.07 - 70.76: 11 70.76 - 88.45: 4 Dihedral angle restraints: 5071 sinusoidal: 1767 harmonic: 3304 Sorted by residual: dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual 180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.62 -66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR A 71 " pdb=" C TYR A 71 " pdb=" N ALA A 72 " pdb=" CA ALA A 72 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 957 0.057 - 0.113: 322 0.113 - 0.169: 80 0.169 - 0.226: 19 0.226 - 0.282: 8 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 270 " pdb=" CA ILE C 270 " pdb=" CG1 ILE C 270 " pdb=" CG2 ILE C 270 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1383 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 176 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 308 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 309 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.037 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 981 2.73 - 3.27: 7741 3.27 - 3.81: 14228 3.81 - 4.36: 17133 4.36 - 4.90: 29082 Nonbonded interactions: 69165 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.187 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 260 " pdb=" OG1 THR B 316 " model vdw 2.252 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.277 3.040 ... (remaining 69160 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 ========== 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=1.00 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: 0.470 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: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.040 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:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.011 0.087 8610 Z= 0.479 Angle : 1.190 13.295 11728 Z= 0.695 Chirality : 0.063 0.282 1386 Planarity : 0.007 0.073 1490 Dihedral : 14.167 88.451 2922 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.17 % Allowed : 10.04 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.69 (0.19), residues: 1121 helix: -4.59 (0.13), residues: 322 sheet: -1.96 (0.28), residues: 272 loop : -2.65 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 154 TYR 0.033 0.003 TYR C 59 PHE 0.037 0.004 PHE C 234 TRP 0.023 0.004 TRP C 99 HIS 0.008 0.002 HIS E 167 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.48 ( 8605) covalent geometry : angle 1.18846 / 0.69 (11717) SS BOND : bond 0.01320 / 0.55 ( 4) SS BOND : angle 2.35036 / 1.30 ( 8) hydrogen bonds : bond 0.30934 / 20.60 ( 286) hydrogen bonds : angle 11.55558 / 7.86 ( 792) link_TRANS : bond 0.00397 / 0.21 ( 1) link_TRANS : angle 0.35169 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7460 (m-80) cc_final: 0.7131 (m-80) REVERT: A 75 LYS cc_start: 0.6087 (mmtm) cc_final: 0.5728 (tptt) REVERT: C 327 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7750 (m) REVERT: E 6 GLU cc_start: 0.7745 (pm20) cc_final: 0.7446 (pm20) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 0.4211 time to fit residues: 92.2173 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.5509 > 50:) overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 102 GLN B 346 ASN C 6 GLN C 62 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.198598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141136 restraints weight = 10653.174| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.77 r_work: 0.3616 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8610 Z= 0.151 Angle : 0.683 11.585 11728 Z= 0.363 Chirality : 0.044 0.205 1386 Planarity : 0.005 0.047 1490 Dihedral : 6.843 53.226 1222 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.03 % Allowed : 18.09 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.72 (0.21), residues: 1121 helix: -3.40 (0.20), residues: 320 sheet: -1.47 (0.29), residues: 272 loop : -2.31 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 155 TYR 0.024 0.002 TYR A 273 PHE 0.016 0.002 PHE C 241 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8605) covalent geometry : angle 0.68306 / 0.36 (11717) SS BOND : bond 0.00492 / 0.19 ( 4) SS BOND : angle 0.78804 / 0.48 ( 8) hydrogen bonds : bond 0.04625 / 3.10 ( 286) hydrogen bonds : angle 6.60499 / 4.55 ( 792) link_TRANS : bond 0.00069 / 0.04 ( 1) link_TRANS : angle 0.14616 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8134 (mp) cc_final: 0.7833 (tt) REVERT: A 163 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7991 (m) REVERT: C 59 TYR cc_start: 0.7673 (m-80) cc_final: 0.7210 (m-80) REVERT: C 241 PHE cc_start: 0.7125 (p90) cc_final: 0.6811 (p90) REVERT: C 243 THR cc_start: 0.8251 (p) cc_final: 0.7915 (p) REVERT: D 21 MET cc_start: 0.6963 (mmt) cc_final: 0.6756 (mmt) REVERT: E 6 GLU cc_start: 0.7702 (pm20) cc_final: 0.7168 (pm20) REVERT: E 19 LYS cc_start: 0.8272 (tttp) cc_final: 0.8034 (ptmm) REVERT: E 20 LEU cc_start: 0.8385 (mp) cc_final: 0.8156 (mt) outliers start: 26 outliers final: 11 residues processed: 189 average time/residue: 0.3896 time to fit residues: 79.7079 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS B 188 HIS C 75 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.198745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140719 restraints weight = 10699.289| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.80 r_work: 0.3620 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 8610 Z= 0.153 Angle : 0.641 10.229 11728 Z= 0.337 Chirality : 0.043 0.159 1386 Planarity : 0.004 0.043 1490 Dihedral : 6.149 53.042 1220 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.72 % Allowed : 18.79 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.07 (0.22), residues: 1121 helix: -2.57 (0.23), residues: 322 sheet: -1.16 (0.29), residues: 267 loop : -2.07 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.012 0.001 TYR E 173 PHE 0.012 0.001 PHE C 241 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 8605) covalent geometry : angle 0.64090 / 0.34 (11717) SS BOND : bond 0.00501 / 0.21 ( 4) SS BOND : angle 0.64689 / 0.38 ( 8) hydrogen bonds : bond 0.03840 / 2.57 ( 286) hydrogen bonds : angle 5.91708 / 4.10 ( 792) link_TRANS : bond 0.00114 / 0.06 ( 1) link_TRANS : angle 0.09564 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8001 (m) REVERT: A 273 TYR cc_start: 0.7882 (m-80) cc_final: 0.7493 (m-80) REVERT: B 22 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8232 (m110) REVERT: B 248 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8295 (mtpp) REVERT: C 44 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6518 (tp-100) REVERT: C 59 TYR cc_start: 0.7679 (m-80) cc_final: 0.7070 (m-80) REVERT: C 61 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7937 (ppp) REVERT: C 241 PHE cc_start: 0.7081 (p90) cc_final: 0.6808 (p90) REVERT: C 252 LEU cc_start: 0.8571 (tt) cc_final: 0.8349 (tp) REVERT: E 6 GLU cc_start: 0.7633 (pm20) cc_final: 0.7098 (pm20) REVERT: E 19 LYS cc_start: 0.8275 (tttp) cc_final: 0.8021 (ptmm) REVERT: E 20 LEU cc_start: 0.8330 (mp) cc_final: 0.8101 (mt) REVERT: E 39 GLN cc_start: 0.8331 (tt0) cc_final: 0.8114 (tt0) REVERT: E 192 MET cc_start: 0.5931 (tmm) cc_final: 0.5341 (tpp) outliers start: 49 outliers final: 24 residues processed: 192 average time/residue: 0.4344 time to fit residues: 90.5853 Evaluate side-chains 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 0.0040 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.202851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147512 restraints weight = 10764.350| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.69 r_work: 0.3683 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8610 Z= 0.109 Angle : 0.605 10.724 11728 Z= 0.312 Chirality : 0.042 0.160 1386 Planarity : 0.004 0.035 1490 Dihedral : 5.602 50.503 1220 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.43 % Allowed : 21.47 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.59 (0.23), residues: 1121 helix: -2.00 (0.26), residues: 323 sheet: -1.01 (0.30), residues: 247 loop : -1.81 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.011 0.001 TYR A 50 PHE 0.012 0.001 PHE B 334 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8605) covalent geometry : angle 0.60478 / 0.31 (11717) SS BOND : bond 0.00291 / 0.12 ( 4) SS BOND : angle 0.41715 / 0.23 ( 8) hydrogen bonds : bond 0.03109 / 2.08 ( 286) hydrogen bonds : angle 5.39461 / 3.73 ( 792) link_TRANS : bond 0.00084 / 0.04 ( 1) link_TRANS : angle 0.11189 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7829 (m) REVERT: B 21 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (ttp80) REVERT: B 297 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7665 (mp0) REVERT: B 326 SER cc_start: 0.8921 (m) cc_final: 0.8639 (p) REVERT: C 44 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6574 (tp-100) REVERT: C 59 TYR cc_start: 0.7370 (m-80) cc_final: 0.6782 (m-80) REVERT: C 241 PHE cc_start: 0.6838 (p90) cc_final: 0.6574 (p90) REVERT: C 243 THR cc_start: 0.8137 (p) cc_final: 0.7888 (p) REVERT: C 290 ASP cc_start: 0.5745 (p0) cc_final: 0.5495 (p0) REVERT: E 6 GLU cc_start: 0.7399 (pm20) cc_final: 0.6974 (pm20) REVERT: E 19 LYS cc_start: 0.8282 (tttp) cc_final: 0.8047 (ptmm) REVERT: E 46 GLU cc_start: 0.7390 (pt0) cc_final: 0.7088 (pp20) REVERT: E 153 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.3232 (pp20) REVERT: E 192 MET cc_start: 0.5486 (tmm) cc_final: 0.5126 (tpp) outliers start: 38 outliers final: 19 residues processed: 194 average time/residue: 0.4443 time to fit residues: 93.2657 Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 62 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.202093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147582 restraints weight = 10780.808| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.00 r_work: 0.3649 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8610 Z= 0.127 Angle : 0.619 9.341 11728 Z= 0.320 Chirality : 0.043 0.178 1386 Planarity : 0.003 0.034 1490 Dihedral : 5.486 50.991 1219 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.32 % Allowed : 23.69 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.36 (0.23), residues: 1121 helix: -1.77 (0.26), residues: 332 sheet: -0.91 (0.29), residues: 272 loop : -1.67 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.017 0.001 TYR A 71 PHE 0.013 0.001 PHE B 334 TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8605) covalent geometry : angle 0.61837 / 0.32 (11717) SS BOND : bond 0.00314 / 0.12 ( 4) SS BOND : angle 0.88523 / 0.54 ( 8) hydrogen bonds : bond 0.03167 / 2.12 ( 286) hydrogen bonds : angle 5.29186 / 3.66 ( 792) link_TRANS : bond 0.00078 / 0.04 ( 1) link_TRANS : angle 0.15282 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7851 (m) REVERT: B 21 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8357 (ttp80) REVERT: B 22 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8142 (m110) REVERT: B 297 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7622 (mp0) REVERT: B 326 SER cc_start: 0.8927 (m) cc_final: 0.8633 (p) REVERT: C 44 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6559 (tp-100) REVERT: C 59 TYR cc_start: 0.7490 (m-80) cc_final: 0.7232 (m-80) REVERT: C 61 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (ppp) REVERT: C 237 ASN cc_start: 0.7976 (t0) cc_final: 0.7670 (t0) REVERT: C 243 THR cc_start: 0.8185 (p) cc_final: 0.7915 (p) REVERT: C 290 ASP cc_start: 0.5649 (p0) cc_final: 0.5410 (p0) REVERT: E 6 GLU cc_start: 0.7462 (pm20) cc_final: 0.7021 (pm20) REVERT: E 19 LYS cc_start: 0.8258 (tttp) cc_final: 0.7997 (ptmm) REVERT: E 140 MET cc_start: 0.4933 (mpp) cc_final: 0.4639 (mpp) REVERT: E 153 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.3218 (pp20) REVERT: E 192 MET cc_start: 0.5368 (tmm) cc_final: 0.5107 (tpp) outliers start: 37 outliers final: 22 residues processed: 184 average time/residue: 0.4343 time to fit residues: 86.4811 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS C 75 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.199633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142048 restraints weight = 10741.800| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.79 r_work: 0.3626 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8610 Z= 0.153 Angle : 0.633 13.728 11728 Z= 0.326 Chirality : 0.044 0.157 1386 Planarity : 0.003 0.040 1490 Dihedral : 5.521 51.536 1219 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.60 % Allowed : 23.22 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.20 (0.24), residues: 1121 helix: -1.56 (0.27), residues: 331 sheet: -0.84 (0.29), residues: 272 loop : -1.62 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.013 0.001 TYR A 312 PHE 0.012 0.001 PHE B 334 TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 8605) covalent geometry : angle 0.63274 / 0.33 (11717) SS BOND : bond 0.00350 / 0.14 ( 4) SS BOND : angle 0.90189 / 0.55 ( 8) hydrogen bonds : bond 0.03216 / 2.17 ( 286) hydrogen bonds : angle 5.20630 / 3.61 ( 792) link_TRANS : bond 0.00101 / 0.05 ( 1) link_TRANS : angle 0.12266 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 312 TYR cc_start: 0.7988 (m-80) cc_final: 0.7495 (m-80) REVERT: B 14 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: B 21 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (ttp80) REVERT: B 297 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7665 (mp0) REVERT: B 326 SER cc_start: 0.8923 (m) cc_final: 0.8628 (p) REVERT: C 59 TYR cc_start: 0.7642 (m-80) cc_final: 0.6872 (m-80) REVERT: C 61 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: C 290 ASP cc_start: 0.5572 (p0) cc_final: 0.5325 (p0) REVERT: E 6 GLU cc_start: 0.7553 (pm20) cc_final: 0.7113 (pm20) REVERT: E 19 LYS cc_start: 0.8279 (tttp) cc_final: 0.8017 (ptmm) REVERT: E 46 GLU cc_start: 0.7322 (pt0) cc_final: 0.7041 (pp20) REVERT: E 140 MET cc_start: 0.4783 (mpp) cc_final: 0.4485 (mpp) REVERT: E 153 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.3231 (pp20) REVERT: E 192 MET cc_start: 0.5472 (tmm) cc_final: 0.5138 (tpp) outliers start: 48 outliers final: 31 residues processed: 191 average time/residue: 0.4370 time to fit residues: 90.4054 Evaluate side-chains 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 48 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140548 restraints weight = 10666.058| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.79 r_work: 0.3594 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8610 Z= 0.115 Angle : 0.610 13.401 11728 Z= 0.315 Chirality : 0.042 0.150 1386 Planarity : 0.003 0.041 1490 Dihedral : 5.316 50.636 1219 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.97 % Allowed : 25.20 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.99 (0.24), residues: 1121 helix: -1.39 (0.27), residues: 333 sheet: -0.75 (0.29), residues: 272 loop : -1.48 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.009 0.001 TYR E 190 PHE 0.021 0.001 PHE C 241 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8605) covalent geometry : angle 0.61018 / 0.31 (11717) SS BOND : bond 0.00317 / 0.13 ( 4) SS BOND : angle 0.68425 / 0.40 ( 8) hydrogen bonds : bond 0.02981 / 2.01 ( 286) hydrogen bonds : angle 5.07151 / 3.52 ( 792) link_TRANS : bond 0.00031 / 0.02 ( 1) link_TRANS : angle 0.18623 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7760 (m) REVERT: B 14 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: B 297 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7597 (mp0) REVERT: B 326 SER cc_start: 0.8938 (m) cc_final: 0.8670 (p) REVERT: C 61 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8113 (ppp) REVERT: C 100 VAL cc_start: 0.8947 (m) cc_final: 0.8609 (p) REVERT: C 243 THR cc_start: 0.7984 (p) cc_final: 0.7748 (p) REVERT: C 290 ASP cc_start: 0.5331 (p0) cc_final: 0.5091 (p0) REVERT: E 6 GLU cc_start: 0.7565 (pm20) cc_final: 0.7089 (pm20) REVERT: E 19 LYS cc_start: 0.8227 (tttp) cc_final: 0.7922 (ptmm) REVERT: E 46 GLU cc_start: 0.7396 (pt0) cc_final: 0.6995 (pp20) REVERT: E 192 MET cc_start: 0.5154 (tmm) cc_final: 0.4811 (tpp) outliers start: 34 outliers final: 21 residues processed: 184 average time/residue: 0.4567 time to fit residues: 90.7152 Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136799 restraints weight = 10639.498| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.85 r_work: 0.3543 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8610 Z= 0.167 Angle : 0.662 12.940 11728 Z= 0.342 Chirality : 0.044 0.159 1386 Planarity : 0.004 0.052 1490 Dihedral : 5.463 51.231 1219 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.43 % Allowed : 25.79 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.24), residues: 1121 helix: -1.31 (0.27), residues: 332 sheet: -0.62 (0.30), residues: 260 loop : -1.53 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 18 TYR 0.012 0.001 TYR E 103 PHE 0.018 0.002 PHE C 292 TRP 0.010 0.001 TRP E 36 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 8605) covalent geometry : angle 0.66208 / 0.34 (11717) SS BOND : bond 0.00387 / 0.16 ( 4) SS BOND : angle 0.89843 / 0.55 ( 8) hydrogen bonds : bond 0.03311 / 2.24 ( 286) hydrogen bonds : angle 5.21791 / 3.60 ( 792) link_TRANS : bond 0.00074 / 0.04 ( 1) link_TRANS : angle 0.17045 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7905 (m) REVERT: B 14 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: B 297 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7626 (mp0) REVERT: B 326 SER cc_start: 0.8945 (m) cc_final: 0.8670 (p) REVERT: C 61 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (ppp) REVERT: C 290 ASP cc_start: 0.5561 (p0) cc_final: 0.5361 (p0) REVERT: E 6 GLU cc_start: 0.7626 (pm20) cc_final: 0.7121 (pm20) REVERT: E 19 LYS cc_start: 0.8240 (tttp) cc_final: 0.7939 (ptmm) REVERT: E 39 GLN cc_start: 0.8282 (tt0) cc_final: 0.8068 (tt0) REVERT: E 140 MET cc_start: 0.4394 (mpp) cc_final: 0.3738 (mpp) REVERT: E 153 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.3406 (pp20) REVERT: E 192 MET cc_start: 0.5455 (tmm) cc_final: 0.4977 (tpp) outliers start: 38 outliers final: 25 residues processed: 168 average time/residue: 0.4328 time to fit residues: 78.8484 Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.196444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139346 restraints weight = 10549.796| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.78 r_work: 0.3577 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8610 Z= 0.129 Angle : 0.642 12.425 11728 Z= 0.329 Chirality : 0.043 0.149 1386 Planarity : 0.004 0.041 1490 Dihedral : 5.369 50.400 1219 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.20 % Allowed : 26.49 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.84 (0.24), residues: 1121 helix: -1.26 (0.27), residues: 348 sheet: -0.55 (0.30), residues: 260 loop : -1.44 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 18 TYR 0.010 0.001 TYR E 103 PHE 0.021 0.001 PHE C 241 TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8605) covalent geometry : angle 0.64177 / 0.33 (11717) SS BOND : bond 0.00313 / 0.12 ( 4) SS BOND : angle 0.96742 / 0.59 ( 8) hydrogen bonds : bond 0.03111 / 2.10 ( 286) hydrogen bonds : angle 5.12014 / 3.54 ( 792) link_TRANS : bond 0.00032 / 0.02 ( 1) link_TRANS : angle 0.16066 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 312 TYR cc_start: 0.7266 (m-10) cc_final: 0.7043 (m-10) REVERT: B 14 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: B 17 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7803 (mtmt) REVERT: B 297 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7659 (mp0) REVERT: B 326 SER cc_start: 0.8933 (m) cc_final: 0.8659 (p) REVERT: C 61 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (ppp) REVERT: C 214 ARG cc_start: 0.7490 (mtm180) cc_final: 0.7123 (mtm180) REVERT: C 243 THR cc_start: 0.7827 (p) cc_final: 0.7594 (p) REVERT: E 6 GLU cc_start: 0.7571 (pm20) cc_final: 0.7066 (pm20) REVERT: E 18 ARG cc_start: 0.6738 (tpt-90) cc_final: 0.6498 (ttt90) REVERT: E 19 LYS cc_start: 0.8218 (tttp) cc_final: 0.7882 (ptmm) REVERT: E 39 GLN cc_start: 0.8243 (tt0) cc_final: 0.8005 (tt0) REVERT: E 46 GLU cc_start: 0.7372 (pt0) cc_final: 0.6998 (pp20) REVERT: E 140 MET cc_start: 0.4562 (mpp) cc_final: 0.3999 (mpp) REVERT: E 153 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.3374 (pp20) REVERT: E 192 MET cc_start: 0.5284 (tmm) cc_final: 0.4846 (tpp) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.4387 time to fit residues: 84.6643 Evaluate side-chains 179 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.198774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142516 restraints weight = 10579.415| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.77 r_work: 0.3616 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8610 Z= 0.112 Angle : 0.621 12.654 11728 Z= 0.317 Chirality : 0.043 0.153 1386 Planarity : 0.003 0.036 1490 Dihedral : 5.177 48.884 1219 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.92 % Allowed : 27.42 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.59 (0.25), residues: 1121 helix: -0.99 (0.28), residues: 347 sheet: -0.63 (0.29), residues: 282 loop : -1.22 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.010 0.001 TYR E 190 PHE 0.013 0.001 PHE B 334 TRP 0.010 0.001 TRP C 99 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8605) covalent geometry : angle 0.62065 / 0.32 (11717) SS BOND : bond 0.00339 / 0.15 ( 4) SS BOND : angle 0.61166 / 0.37 ( 8) hydrogen bonds : bond 0.02927 / 1.97 ( 286) hydrogen bonds : angle 5.02031 / 3.47 ( 792) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.22045 / 0.11 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7545 (m) REVERT: A 170 SER cc_start: 0.8597 (p) cc_final: 0.8378 (p) REVERT: B 14 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: B 297 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7686 (mp0) REVERT: B 326 SER cc_start: 0.9003 (m) cc_final: 0.8708 (p) REVERT: C 61 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8162 (ppp) REVERT: C 214 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7163 (mtm180) REVERT: C 243 THR cc_start: 0.7732 (p) cc_final: 0.7487 (p) REVERT: E 6 GLU cc_start: 0.7552 (pm20) cc_final: 0.7053 (pm20) REVERT: E 18 ARG cc_start: 0.6747 (tpt-90) cc_final: 0.5847 (ttt90) REVERT: E 19 LYS cc_start: 0.8215 (tttp) cc_final: 0.7897 (ptmm) REVERT: E 46 GLU cc_start: 0.7310 (pt0) cc_final: 0.6933 (pp20) REVERT: E 140 MET cc_start: 0.4529 (mpp) cc_final: 0.3895 (mpp) REVERT: E 173 TYR cc_start: 0.7936 (m-10) cc_final: 0.7693 (m-10) REVERT: E 192 MET cc_start: 0.5240 (tmm) cc_final: 0.4883 (tpp) outliers start: 25 outliers final: 19 residues processed: 174 average time/residue: 0.4148 time to fit residues: 78.6359 Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141610 restraints weight = 10538.273| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.84 r_work: 0.3657 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8610 Z= 0.113 Angle : 0.627 12.330 11728 Z= 0.319 Chirality : 0.043 0.172 1386 Planarity : 0.003 0.035 1490 Dihedral : 5.135 48.628 1219 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.92 % Allowed : 28.00 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.48 (0.25), residues: 1121 helix: -0.88 (0.28), residues: 349 sheet: -0.56 (0.29), residues: 282 loop : -1.16 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.010 0.001 TYR E 190 PHE 0.025 0.001 PHE C 241 TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 8605) covalent geometry : angle 0.62719 / 0.32 (11717) SS BOND : bond 0.00320 / 0.13 ( 4) SS BOND : angle 0.58103 / 0.36 ( 8) hydrogen bonds : bond 0.02939 / 1.98 ( 286) hydrogen bonds : angle 4.97283 / 3.43 ( 792) link_TRANS : bond 0.00024 / 0.01 ( 1) link_TRANS : angle 0.24234 / 0.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3180.17 seconds wall clock time: 55 minutes 8.81 seconds (3308.81 seconds total)