Starting phenix.real_space_refine on Thu Jul 2 13:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.map" model { file = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aue_11927/07_2026/7aue_11927.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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 69 5.16 5 C 5580 2.51 5 N 1499 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2050 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1747 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'ACE': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.18 Number of scatterers: 8755 At special positions: 0 Unit cell: (103.2, 121.26, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 69 16.00 O 1606 8.00 N 1499 7.00 C 5580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied TRANS " DAL C 4 " - " CYS C 3 " " DPN C 6 " - " HIS C 5 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL C 4 " pdb=" CB DPN C 6 " Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 33.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'R' and resid 47 through 51 removed outlier: 3.625A pdb=" N VAL R 50 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 72 removed outlier: 3.804A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 76 removed outlier: 3.743A pdb=" N HIS R 76 " --> pdb=" O LYS R 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 73 through 76' Processing helix chain 'R' and resid 77 through 96 removed outlier: 3.503A pdb=" N PHE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS R 84 " --> pdb=" O TYR R 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 108 removed outlier: 3.575A pdb=" N THR R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE R 104 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 124 through 153 removed outlier: 3.574A pdb=" N LEU R 134 " --> pdb=" O CYS R 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 140 " --> pdb=" O SER R 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 186 removed outlier: 3.668A pdb=" N ILE R 168 " --> pdb=" O LYS R 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER R 171 " --> pdb=" O GLY R 167 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP R 174 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR R 178 " --> pdb=" O TRP R 174 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY R 181 " --> pdb=" O CYS R 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE R 185 " --> pdb=" O GLY R 181 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 203 removed outlier: 3.615A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 215 removed outlier: 4.378A pdb=" N SER R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 225 removed outlier: 3.599A pdb=" N LYS R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 251 removed outlier: 3.762A pdb=" N THR R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU R 247 " --> pdb=" O GLY R 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 271 removed outlier: 3.639A pdb=" N TRP R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O PRO R 260 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE R 266 " --> pdb=" O PHE R 262 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 281 removed outlier: 3.750A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 287 removed outlier: 5.993A pdb=" N ASN R 285 " --> pdb=" O SER R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 302 removed outlier: 3.721A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.698A pdb=" N LYS R 311 " --> pdb=" O GLN R 307 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 312 " --> pdb=" O GLU R 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.832A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.524A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.632A pdb=" N SER A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 4.137A pdb=" N ARG A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.948A pdb=" N GLU A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.102A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 removed outlier: 3.595A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 370 removed outlier: 3.855A pdb=" N ASP A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.510A pdb=" N ASN B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.509A pdb=" N THR B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 removed outlier: 3.657A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.627A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.751A pdb=" N PHE A 191 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL A 203 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG A 35 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE A 224 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 37 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 226 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 223 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 269 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 225 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASN A 271 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 227 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 69 removed outlier: 4.295A pdb=" N PHE B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 348 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 334 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 80 removed outlier: 3.719A pdb=" N ALA B 77 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS B 108 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP B 100 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 106 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 122 removed outlier: 6.088A pdb=" N CYS B 138 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU B 155 " --> pdb=" O CYS B 138 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 140 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 151 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 4.096A pdb=" N CYS B 165 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 174 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 195 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 187 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 193 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 209 removed outlier: 3.689A pdb=" N SER B 206 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 237 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP B 229 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS B 235 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.678A pdb=" N GLY B 261 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 249 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 259 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 251 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA B 257 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 279 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 271 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.499A pdb=" N GLY B 305 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 293 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 303 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N PHE B 295 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 301 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 311 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 324 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B 313 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 320 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.626A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.780A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 888 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: 0.94 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2452 1.44 - 1.56: 4974 1.56 - 1.69: 1 1.69 - 1.82: 100 Bond restraints: 8927 Sorted by residual: bond pdb=" C ARG C 7 " pdb=" N TRP C 8 " ideal model delta sigma weight residual 1.329 1.470 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" C DPN C 6 " pdb=" N ARG C 7 " ideal model delta sigma weight residual 1.329 1.461 -0.132 1.40e-02 5.10e+03 8.88e+01 bond pdb=" CZ ARG C 2 " pdb=" NH1 ARG C 2 " ideal model delta sigma weight residual 1.323 1.453 -0.130 1.40e-02 5.10e+03 8.64e+01 bond pdb=" CZ ARG C 7 " pdb=" NH2 ARG C 7 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.30e-02 5.92e+03 8.57e+01 bond pdb=" CZ ARG C 2 " pdb=" NH2 ARG C 2 " ideal model delta sigma weight residual 1.330 1.449 -0.119 1.30e-02 5.92e+03 8.45e+01 ... (remaining 8922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 11862 2.28 - 4.55: 198 4.55 - 6.83: 23 6.83 - 9.11: 10 9.11 - 11.38: 4 Bond angle restraints: 12097 Sorted by residual: angle pdb=" C LYS B 297 " pdb=" N SER B 298 " pdb=" CA SER B 298 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" N GLY B 133 " pdb=" CA GLY B 133 " pdb=" C GLY B 133 " ideal model delta sigma weight residual 110.43 117.61 -7.18 1.35e+00 5.49e-01 2.83e+01 angle pdb=" C ARG A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" N VAL R 228 " pdb=" CA VAL R 228 " pdb=" C VAL R 228 " ideal model delta sigma weight residual 112.80 108.50 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" N TYR A 297 " pdb=" CA TYR A 297 " pdb=" C TYR A 297 " ideal model delta sigma weight residual 110.80 118.49 -7.69 2.13e+00 2.20e-01 1.30e+01 ... (remaining 12092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 5230 35.97 - 71.95: 64 71.95 - 107.92: 6 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 5301 sinusoidal: 2020 harmonic: 3281 Sorted by residual: dihedral pdb=" CH3 ACE C 1 " pdb=" C ACE C 1 " pdb=" N ARG C 2 " pdb=" CA ARG C 2 " ideal model delta sinusoidal sigma weight residual 180.00 0.13 179.87 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA LYS B 297 " pdb=" C LYS B 297 " pdb=" N SER B 298 " pdb=" CA SER B 298 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -121.09 35.09 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 5298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1049 0.054 - 0.109: 275 0.109 - 0.163: 67 0.163 - 0.218: 5 0.218 - 0.272: 1 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA TYR A 297 " pdb=" N TYR A 297 " pdb=" C TYR A 297 " pdb=" CB TYR A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ARG C 7 " pdb=" N ARG C 7 " pdb=" C ARG C 7 " pdb=" CB ARG C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CG LEU B 86 " pdb=" CB LEU B 86 " pdb=" CD1 LEU B 86 " pdb=" CD2 LEU B 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1394 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 298 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO R 299 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 259 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO R 260 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 77 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO R 78 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 78 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 78 " 0.035 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 65 2.64 - 3.21: 6820 3.21 - 3.77: 12253 3.77 - 4.34: 17855 4.34 - 4.90: 29518 Nonbonded interactions: 66511 Sorted by model distance: nonbonded pdb=" OD1 ASP R 126 " pdb="CA CA R 501 " model vdw 2.077 2.510 nonbonded pdb=" OD2 ASP R 126 " pdb="CA CA R 501 " model vdw 2.142 2.510 nonbonded pdb=" OE2 GLU R 100 " pdb="CA CA R 501 " model vdw 2.297 2.510 nonbonded pdb=" OH TYR R 80 " pdb=" OG SER R 306 " model vdw 2.331 3.040 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.352 3.040 ... (remaining 66506 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: 1.260 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: 0.030 Set scattering table: 0.020 Process input model: 6.820 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:5.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.006 0.141 8934 Z= 0.425 Angle : 0.804 11.384 12111 Z= 0.450 Chirality : 0.052 0.272 1397 Planarity : 0.006 0.066 1523 Dihedral : 14.186 179.865 3161 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.20), residues: 1101 helix: -4.76 (0.10), residues: 381 sheet: -1.12 (0.30), residues: 264 loop : -2.23 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.028 0.002 TYR A 297 PHE 0.022 0.002 PHE B 216 TRP 0.009 0.001 TRP B 228 HIS 0.011 0.002 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.39 ( 8927) covalent geometry : angle 0.80243 / 0.45 (12097) SS BOND : bond 0.00492 / 0.25 ( 4) SS BOND : angle 1.06597 / 0.61 ( 8) hydrogen bonds : bond 0.32177 / 21.54 ( 311) hydrogen bonds : angle 9.81489 / 7.05 ( 888) Misc. bond : bond 0.09497 / 5.00 ( 1) link_TRANS : bond 0.12946 / 6.51 ( 2) link_TRANS : angle 2.54486 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.201 Fit side-chains REVERT: R 215 MET cc_start: 0.8564 (mtp) cc_final: 0.8312 (mtp) REVERT: R 242 LYS cc_start: 0.7786 (tttp) cc_final: 0.7415 (tttm) REVERT: R 281 MET cc_start: 0.6996 (mtm) cc_final: 0.6730 (mtt) REVERT: R 310 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7644 (ttp80) REVERT: R 311 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7388 (mttt) REVERT: A 199 HIS cc_start: 0.6932 (t-90) cc_final: 0.6516 (t-170) REVERT: A 301 GLU cc_start: 0.5476 (pm20) cc_final: 0.5197 (tm-30) REVERT: B 93 ASP cc_start: 0.7857 (p0) cc_final: 0.7541 (p0) REVERT: B 118 MET cc_start: 0.8630 (mtp) cc_final: 0.8207 (mtm) REVERT: B 284 ASP cc_start: 0.7222 (m-30) cc_final: 0.7020 (m-30) REVERT: G 47 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7138 (tt0) REVERT: S 128 MET cc_start: 0.8457 (mmm) cc_final: 0.8035 (mmt) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.4689 time to fit residues: 86.1746 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 62 ASN R 294 ASN A 192 GLN A 197 ASN A 273 GLN B 33 ASN B 254 ASN S 13 GLN S 113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107491 restraints weight = 10828.115| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.98 r_work: 0.3089 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8934 Z= 0.099 Angle : 0.547 9.574 12111 Z= 0.294 Chirality : 0.043 0.197 1397 Planarity : 0.004 0.043 1523 Dihedral : 7.296 179.111 1225 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.39 % Allowed : 13.11 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.23), residues: 1101 helix: -3.25 (0.19), residues: 369 sheet: -0.55 (0.30), residues: 274 loop : -1.68 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.026 0.001 TYR A 297 PHE 0.014 0.001 PHE B 216 TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 8927) covalent geometry : angle 0.54709 / 0.29 (12097) SS BOND : bond 0.00373 / 0.19 ( 4) SS BOND : angle 0.73021 / 0.43 ( 8) hydrogen bonds : bond 0.04701 / 3.11 ( 311) hydrogen bonds : angle 5.23969 / 3.73 ( 888) Misc. bond : bond 0.00019 / 0.01 ( 1) link_TRANS : bond 0.00161 / 0.08 ( 2) link_TRANS : angle 0.40688 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.213 Fit side-chains REVERT: R 200 MET cc_start: 0.7728 (mtt) cc_final: 0.7331 (mtt) REVERT: R 204 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6838 (mpp) REVERT: R 215 MET cc_start: 0.8620 (mtp) cc_final: 0.8416 (mtp) REVERT: R 242 LYS cc_start: 0.8059 (tttp) cc_final: 0.7661 (tttm) REVERT: R 281 MET cc_start: 0.7361 (mtm) cc_final: 0.6943 (mtt) REVERT: R 310 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7502 (ttp80) REVERT: R 311 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7356 (mttt) REVERT: A 24 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6736 (mtm110) REVERT: A 199 HIS cc_start: 0.7611 (t-90) cc_final: 0.7053 (t-170) REVERT: A 234 MET cc_start: 0.7213 (mtp) cc_final: 0.6910 (mtt) REVERT: A 301 GLU cc_start: 0.5514 (pm20) cc_final: 0.4974 (tm-30) REVERT: A 351 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7029 (pp) REVERT: B 37 ASP cc_start: 0.7596 (m-30) cc_final: 0.7342 (m-30) REVERT: B 93 ASP cc_start: 0.8063 (p0) cc_final: 0.7709 (p0) REVERT: B 118 MET cc_start: 0.9003 (mtp) cc_final: 0.8632 (mtm) REVERT: G 42 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7470 (tm-30) REVERT: G 47 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7446 (tt0) REVERT: S 87 ARG cc_start: 0.7101 (mtt90) cc_final: 0.6899 (mtt90) REVERT: S 93 MET cc_start: 0.8385 (ttm) cc_final: 0.8093 (ttt) outliers start: 13 outliers final: 0 residues processed: 152 average time/residue: 0.5319 time to fit residues: 85.3013 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 351 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104447 restraints weight = 10772.303| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.87 r_work: 0.3056 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8934 Z= 0.109 Angle : 0.547 10.022 12111 Z= 0.290 Chirality : 0.044 0.197 1397 Planarity : 0.004 0.033 1523 Dihedral : 6.906 178.398 1221 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.92 % Allowed : 15.88 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.24), residues: 1101 helix: -2.18 (0.24), residues: 376 sheet: -0.02 (0.31), residues: 273 loop : -1.52 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.024 0.001 TYR A 297 PHE 0.013 0.001 PHE B 216 TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8927) covalent geometry : angle 0.54653 / 0.29 (12097) SS BOND : bond 0.00648 / 0.32 ( 4) SS BOND : angle 0.81750 / 0.50 ( 8) hydrogen bonds : bond 0.04575 / 3.00 ( 311) hydrogen bonds : angle 4.79030 / 3.37 ( 888) Misc. bond : bond 0.00154 / 0.08 ( 1) link_TRANS : bond 0.00194 / 0.10 ( 2) link_TRANS : angle 0.68876 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 46 VAL cc_start: 0.8350 (p) cc_final: 0.8090 (t) REVERT: R 200 MET cc_start: 0.7668 (mtt) cc_final: 0.7201 (mtt) REVERT: R 204 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.6873 (mpp) REVERT: R 215 MET cc_start: 0.8653 (mtp) cc_final: 0.8452 (mtp) REVERT: R 242 LYS cc_start: 0.8085 (tttp) cc_final: 0.7732 (tttm) REVERT: R 281 MET cc_start: 0.7408 (mtm) cc_final: 0.7045 (mtt) REVERT: R 310 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7408 (ttp80) REVERT: R 311 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7363 (mttt) REVERT: A 24 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6755 (mtm110) REVERT: A 234 MET cc_start: 0.7286 (mtp) cc_final: 0.6992 (mtt) REVERT: A 301 GLU cc_start: 0.5539 (pm20) cc_final: 0.5004 (tm-30) REVERT: A 351 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.7021 (pp) REVERT: B 37 ASP cc_start: 0.7616 (m-30) cc_final: 0.7374 (m-30) REVERT: B 93 ASP cc_start: 0.8122 (p0) cc_final: 0.7793 (p0) REVERT: B 118 MET cc_start: 0.9007 (mtp) cc_final: 0.8631 (mtm) REVERT: G 42 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7591 (tm-30) REVERT: G 47 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7495 (tt0) REVERT: S 93 MET cc_start: 0.8400 (ttm) cc_final: 0.8090 (ttt) REVERT: S 128 MET cc_start: 0.8405 (mmm) cc_final: 0.8102 (mmt) outliers start: 18 outliers final: 5 residues processed: 141 average time/residue: 0.5370 time to fit residues: 80.1282 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 3 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 274 ASN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107100 restraints weight = 10970.374| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.02 r_work: 0.3084 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 8934 Z= 0.098 Angle : 0.522 10.640 12111 Z= 0.277 Chirality : 0.043 0.182 1397 Planarity : 0.003 0.035 1523 Dihedral : 6.757 178.891 1221 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 16.10 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.25), residues: 1101 helix: -1.48 (0.26), residues: 376 sheet: 0.15 (0.31), residues: 280 loop : -1.30 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.021 0.001 TYR A 297 PHE 0.013 0.001 PHE B 216 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 8927) covalent geometry : angle 0.52199 / 0.28 (12097) SS BOND : bond 0.00565 / 0.28 ( 4) SS BOND : angle 0.73451 / 0.44 ( 8) hydrogen bonds : bond 0.03897 / 2.56 ( 311) hydrogen bonds : angle 4.42633 / 3.09 ( 888) Misc. bond : bond 0.00059 / 0.03 ( 1) link_TRANS : bond 0.00116 / 0.06 ( 2) link_TRANS : angle 0.56555 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.236 Fit side-chains REVERT: R 200 MET cc_start: 0.7580 (mtt) cc_final: 0.6941 (mtt) REVERT: R 204 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6896 (mpp) REVERT: R 242 LYS cc_start: 0.8095 (tttp) cc_final: 0.7595 (tttm) REVERT: R 281 MET cc_start: 0.7411 (mtm) cc_final: 0.7036 (mtt) REVERT: R 310 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7334 (ttp80) REVERT: R 311 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7351 (mttt) REVERT: A 24 ARG cc_start: 0.7244 (mtt-85) cc_final: 0.6995 (mtm-85) REVERT: A 234 MET cc_start: 0.7190 (mtp) cc_final: 0.6893 (mtt) REVERT: A 286 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7775 (tttt) REVERT: A 301 GLU cc_start: 0.5413 (pm20) cc_final: 0.4877 (pp20) REVERT: B 29 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6373 (tp30) REVERT: B 37 ASP cc_start: 0.7706 (m-30) cc_final: 0.7452 (m-30) REVERT: B 118 MET cc_start: 0.8987 (mtp) cc_final: 0.8613 (mtm) REVERT: G 42 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7644 (tm-30) REVERT: G 47 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7472 (tt0) REVERT: S 87 ARG cc_start: 0.7376 (mtt90) cc_final: 0.6464 (mtt90) REVERT: S 93 MET cc_start: 0.8371 (ttm) cc_final: 0.8040 (ttt) REVERT: S 128 MET cc_start: 0.8369 (mmm) cc_final: 0.8116 (mmt) REVERT: S 207 LEU cc_start: 0.6921 (mp) cc_final: 0.6609 (pt) REVERT: C 2 ARG cc_start: 0.4787 (OUTLIER) cc_final: 0.3756 (tpt-90) outliers start: 17 outliers final: 3 residues processed: 143 average time/residue: 0.5644 time to fit residues: 85.2161 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105312 restraints weight = 10814.370| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.74 r_work: 0.3021 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8934 Z= 0.146 Angle : 0.594 10.285 12111 Z= 0.314 Chirality : 0.046 0.170 1397 Planarity : 0.004 0.034 1523 Dihedral : 6.965 177.863 1221 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.24 % Allowed : 16.31 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1101 helix: -1.41 (0.26), residues: 373 sheet: 0.32 (0.31), residues: 279 loop : -1.18 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.020 0.002 TYR R 268 PHE 0.015 0.002 PHE B 216 TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8927) covalent geometry : angle 0.59348 / 0.31 (12097) SS BOND : bond 0.00775 / 0.39 ( 4) SS BOND : angle 0.96258 / 0.57 ( 8) hydrogen bonds : bond 0.04885 / 3.20 ( 311) hydrogen bonds : angle 4.65589 / 3.24 ( 888) Misc. bond : bond 0.00052 / 0.03 ( 1) link_TRANS : bond 0.00099 / 0.05 ( 2) link_TRANS : angle 0.63879 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.235 Fit side-chains REVERT: R 200 MET cc_start: 0.7628 (mtt) cc_final: 0.6772 (mtt) REVERT: R 204 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7067 (mpp) REVERT: R 242 LYS cc_start: 0.8118 (tttp) cc_final: 0.7702 (tttm) REVERT: R 281 MET cc_start: 0.7478 (mtm) cc_final: 0.7163 (mtt) REVERT: R 310 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7445 (ttp80) REVERT: R 311 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7408 (mttt) REVERT: A 232 TYR cc_start: 0.7797 (p90) cc_final: 0.7590 (p90) REVERT: A 234 MET cc_start: 0.7348 (mtp) cc_final: 0.7033 (mtt) REVERT: A 286 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7795 (tttt) REVERT: A 288 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5590 (tp30) REVERT: A 297 TYR cc_start: 0.5606 (t80) cc_final: 0.5338 (t80) REVERT: A 301 GLU cc_start: 0.5496 (pm20) cc_final: 0.4961 (pp20) REVERT: B 29 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6499 (tp30) REVERT: B 37 ASP cc_start: 0.7624 (m-30) cc_final: 0.7411 (m-30) REVERT: B 118 MET cc_start: 0.9009 (mtp) cc_final: 0.8641 (mtm) REVERT: G 22 GLU cc_start: 0.7111 (tt0) cc_final: 0.6415 (mt-10) REVERT: G 42 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7687 (tm-30) REVERT: G 47 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7566 (tt0) REVERT: S 93 MET cc_start: 0.8469 (ttm) cc_final: 0.8185 (ttt) REVERT: S 207 LEU cc_start: 0.7285 (mp) cc_final: 0.6769 (pt) outliers start: 21 outliers final: 7 residues processed: 141 average time/residue: 0.5278 time to fit residues: 78.5917 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107498 restraints weight = 10853.326| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.84 r_work: 0.3118 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 8934 Z= 0.104 Angle : 0.534 10.345 12111 Z= 0.282 Chirality : 0.043 0.165 1397 Planarity : 0.003 0.047 1523 Dihedral : 6.804 179.145 1221 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.03 % Allowed : 17.70 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1101 helix: -1.03 (0.27), residues: 371 sheet: 0.37 (0.31), residues: 281 loop : -1.05 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.021 0.001 TYR R 268 PHE 0.014 0.001 PHE B 216 TRP 0.009 0.001 TRP S 47 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 8927) covalent geometry : angle 0.53381 / 0.28 (12097) SS BOND : bond 0.00599 / 0.30 ( 4) SS BOND : angle 0.73185 / 0.44 ( 8) hydrogen bonds : bond 0.03953 / 2.59 ( 311) hydrogen bonds : angle 4.32391 / 3.02 ( 888) Misc. bond : bond 0.00049 / 0.03 ( 1) link_TRANS : bond 0.00114 / 0.06 ( 2) link_TRANS : angle 0.55434 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.225 Fit side-chains REVERT: R 204 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7026 (mpp) REVERT: R 242 LYS cc_start: 0.8134 (tttp) cc_final: 0.7792 (tttm) REVERT: R 281 MET cc_start: 0.7451 (mtm) cc_final: 0.7104 (mtt) REVERT: R 310 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7431 (ttp80) REVERT: R 311 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7351 (mttt) REVERT: A 24 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.6881 (ttm110) REVERT: A 232 TYR cc_start: 0.7738 (p90) cc_final: 0.7531 (p90) REVERT: A 234 MET cc_start: 0.7292 (mtp) cc_final: 0.6998 (mtt) REVERT: A 288 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5624 (tp30) REVERT: A 297 TYR cc_start: 0.5625 (t80) cc_final: 0.5423 (t80) REVERT: A 301 GLU cc_start: 0.5528 (pm20) cc_final: 0.4955 (pp20) REVERT: B 29 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6603 (tp30) REVERT: B 37 ASP cc_start: 0.7557 (m-30) cc_final: 0.7223 (m-30) REVERT: B 118 MET cc_start: 0.8967 (mtp) cc_final: 0.8603 (mtm) REVERT: G 47 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7449 (tt0) REVERT: S 93 MET cc_start: 0.8415 (ttm) cc_final: 0.8130 (ttt) REVERT: S 207 LEU cc_start: 0.7156 (mp) cc_final: 0.6824 (pt) REVERT: C 2 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.3536 (tpt-90) outliers start: 19 outliers final: 6 residues processed: 138 average time/residue: 0.5516 time to fit residues: 80.6954 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 52 optimal weight: 0.0030 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 254 ASN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110433 restraints weight = 10773.948| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.84 r_work: 0.3097 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 8934 Z= 0.088 Angle : 0.499 10.399 12111 Z= 0.262 Chirality : 0.042 0.152 1397 Planarity : 0.003 0.047 1523 Dihedral : 6.597 179.562 1221 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 17.91 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 1101 helix: -0.64 (0.28), residues: 372 sheet: 0.55 (0.31), residues: 273 loop : -0.90 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.021 0.001 TYR R 268 PHE 0.013 0.001 PHE B 216 TRP 0.009 0.001 TRP B 228 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 8927) covalent geometry : angle 0.49908 / 0.26 (12097) SS BOND : bond 0.00469 / 0.23 ( 4) SS BOND : angle 0.59980 / 0.36 ( 8) hydrogen bonds : bond 0.03256 / 2.14 ( 311) hydrogen bonds : angle 4.00600 / 2.81 ( 888) Misc. bond : bond 0.00032 / 0.02 ( 1) link_TRANS : bond 0.00119 / 0.06 ( 2) link_TRANS : angle 0.54774 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.256 Fit side-chains REVERT: R 204 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7046 (mpp) REVERT: R 242 LYS cc_start: 0.8123 (tttp) cc_final: 0.7615 (tttm) REVERT: R 281 MET cc_start: 0.7487 (mtm) cc_final: 0.7119 (mtt) REVERT: R 310 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7354 (ttp80) REVERT: R 311 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7382 (mttt) REVERT: A 199 HIS cc_start: 0.7591 (t-90) cc_final: 0.6941 (m170) REVERT: A 201 PHE cc_start: 0.8113 (m-80) cc_final: 0.7551 (m-80) REVERT: A 234 MET cc_start: 0.7157 (mtp) cc_final: 0.6877 (mtt) REVERT: A 301 GLU cc_start: 0.5496 (pm20) cc_final: 0.4941 (pp20) REVERT: B 29 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6510 (tp30) REVERT: B 37 ASP cc_start: 0.7547 (m-30) cc_final: 0.7269 (m-30) REVERT: B 118 MET cc_start: 0.8968 (mtp) cc_final: 0.8597 (mtm) REVERT: G 22 GLU cc_start: 0.7049 (tt0) cc_final: 0.6388 (mt-10) REVERT: G 47 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7422 (tt0) REVERT: S 93 MET cc_start: 0.8411 (ttm) cc_final: 0.8119 (ttt) REVERT: C 2 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.2967 (tpm170) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.5681 time to fit residues: 85.8488 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106598 restraints weight = 10739.493| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.83 r_work: 0.3050 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 8934 Z= 0.129 Angle : 0.571 10.377 12111 Z= 0.301 Chirality : 0.045 0.161 1397 Planarity : 0.004 0.046 1523 Dihedral : 6.773 178.167 1221 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.60 % Allowed : 19.30 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1101 helix: -0.75 (0.27), residues: 375 sheet: 0.54 (0.30), residues: 279 loop : -0.84 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.023 0.002 TYR R 268 PHE 0.015 0.002 PHE B 216 TRP 0.010 0.001 TRP B 99 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8927) covalent geometry : angle 0.57083 / 0.30 (12097) SS BOND : bond 0.00696 / 0.35 ( 4) SS BOND : angle 0.89910 / 0.52 ( 8) hydrogen bonds : bond 0.04287 / 2.80 ( 311) hydrogen bonds : angle 4.29116 / 3.00 ( 888) Misc. bond : bond 0.00058 / 0.03 ( 1) link_TRANS : bond 0.00106 / 0.06 ( 2) link_TRANS : angle 0.58949 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.211 Fit side-chains REVERT: R 242 LYS cc_start: 0.8182 (tttp) cc_final: 0.7700 (tttm) REVERT: R 281 MET cc_start: 0.7422 (mtm) cc_final: 0.7080 (mtt) REVERT: R 310 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7458 (ttp-170) REVERT: R 311 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7365 (mttt) REVERT: A 24 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.6946 (ttm110) REVERT: A 199 HIS cc_start: 0.7597 (t-90) cc_final: 0.6988 (m170) REVERT: A 234 MET cc_start: 0.7198 (mtp) cc_final: 0.6897 (mtt) REVERT: A 297 TYR cc_start: 0.5593 (t80) cc_final: 0.5281 (t80) REVERT: A 301 GLU cc_start: 0.5573 (pm20) cc_final: 0.4958 (pp20) REVERT: A 353 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7301 (mtp180) REVERT: B 29 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6567 (tp30) REVERT: B 37 ASP cc_start: 0.7513 (m-30) cc_final: 0.7248 (m-30) REVERT: B 118 MET cc_start: 0.8996 (mtp) cc_final: 0.8616 (mtm) REVERT: G 22 GLU cc_start: 0.7103 (tt0) cc_final: 0.6502 (mt-10) REVERT: G 47 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7446 (tt0) REVERT: S 93 MET cc_start: 0.8437 (ttm) cc_final: 0.8155 (ttt) REVERT: S 207 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6212 (pp) REVERT: C 2 ARG cc_start: 0.4625 (OUTLIER) cc_final: 0.3481 (tpt-90) outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 0.5818 time to fit residues: 85.9875 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 264 HIS A 52 GLN B 254 ASN G 24 ASN S 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103849 restraints weight = 10815.704| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 8934 Z= 0.192 Angle : 0.659 10.361 12111 Z= 0.348 Chirality : 0.048 0.176 1397 Planarity : 0.004 0.046 1523 Dihedral : 7.086 176.884 1221 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.81 % Allowed : 19.19 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1101 helix: -1.08 (0.26), residues: 374 sheet: 0.45 (0.30), residues: 279 loop : -0.94 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.023 0.002 TYR R 268 PHE 0.018 0.002 PHE B 216 TRP 0.012 0.002 TRP B 99 HIS 0.006 0.001 HIS R 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 8927) covalent geometry : angle 0.65906 / 0.35 (12097) SS BOND : bond 0.00894 / 0.45 ( 4) SS BOND : angle 1.09794 / 0.63 ( 8) hydrogen bonds : bond 0.05381 / 3.53 ( 311) hydrogen bonds : angle 4.69341 / 3.27 ( 888) Misc. bond : bond 0.00084 / 0.04 ( 1) link_TRANS : bond 0.00085 / 0.04 ( 2) link_TRANS : angle 0.62816 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.277 Fit side-chains REVERT: R 242 LYS cc_start: 0.8172 (tttp) cc_final: 0.7785 (tttm) REVERT: R 281 MET cc_start: 0.7445 (mtm) cc_final: 0.7124 (mtt) REVERT: R 310 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7475 (ttp-170) REVERT: R 311 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7358 (mttt) REVERT: A 234 MET cc_start: 0.7223 (mtp) cc_final: 0.6877 (mtt) REVERT: A 301 GLU cc_start: 0.5597 (pm20) cc_final: 0.4980 (pp20) REVERT: A 353 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7340 (mtp180) REVERT: B 29 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6504 (tp30) REVERT: B 118 MET cc_start: 0.9026 (mtp) cc_final: 0.8666 (mtm) REVERT: G 22 GLU cc_start: 0.7107 (tt0) cc_final: 0.6486 (mt-10) REVERT: G 47 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7484 (tt0) REVERT: S 65 LYS cc_start: 0.7606 (tptt) cc_final: 0.7297 (tttp) REVERT: S 93 MET cc_start: 0.8511 (ttm) cc_final: 0.8235 (ttt) REVERT: S 207 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6429 (pp) REVERT: C 2 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.3534 (tpt-90) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 0.5366 time to fit residues: 81.0431 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.0050 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 254 ASN G 24 ASN S 13 GLN S 113 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109309 restraints weight = 10762.383| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.84 r_work: 0.3085 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.104 8934 Z= 0.096 Angle : 0.524 10.278 12111 Z= 0.275 Chirality : 0.043 0.153 1397 Planarity : 0.003 0.056 1523 Dihedral : 6.712 179.289 1221 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.17 % Allowed : 19.72 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.26), residues: 1101 helix: -0.56 (0.28), residues: 378 sheet: 0.59 (0.31), residues: 278 loop : -0.82 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.023 0.001 TYR R 268 PHE 0.014 0.001 PHE B 216 TRP 0.011 0.001 TRP B 228 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8927) covalent geometry : angle 0.52352 / 0.28 (12097) SS BOND : bond 0.00492 / 0.25 ( 4) SS BOND : angle 0.55656 / 0.32 ( 8) hydrogen bonds : bond 0.03466 / 2.28 ( 311) hydrogen bonds : angle 4.11705 / 2.89 ( 888) Misc. bond : bond 0.00031 / 0.02 ( 1) link_TRANS : bond 0.00126 / 0.07 ( 2) link_TRANS : angle 0.53871 / 0.30 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.216 Fit side-chains REVERT: R 242 LYS cc_start: 0.8208 (tttp) cc_final: 0.7716 (tttm) REVERT: R 310 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7370 (ttp80) REVERT: R 311 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7388 (mttt) REVERT: A 24 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.6926 (ttm110) REVERT: A 199 HIS cc_start: 0.7610 (t-90) cc_final: 0.6985 (m170) REVERT: A 234 MET cc_start: 0.7177 (mtp) cc_final: 0.6898 (mtt) REVERT: A 293 GLU cc_start: 0.8100 (tp30) cc_final: 0.7869 (mm-30) REVERT: A 301 GLU cc_start: 0.5484 (pm20) cc_final: 0.4959 (pp20) REVERT: B 118 MET cc_start: 0.8981 (mtp) cc_final: 0.8623 (mtm) REVERT: B 214 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7337 (mtp85) REVERT: G 22 GLU cc_start: 0.7076 (tt0) cc_final: 0.6392 (mt-10) REVERT: G 47 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7377 (tt0) REVERT: S 65 LYS cc_start: 0.7558 (tptt) cc_final: 0.7237 (tttp) REVERT: S 93 MET cc_start: 0.8423 (ttm) cc_final: 0.8132 (ttt) REVERT: C 2 ARG cc_start: 0.4599 (OUTLIER) cc_final: 0.3495 (tpt-90) outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 0.5970 time to fit residues: 88.7500 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 273 GLN B 254 ASN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107399 restraints weight = 10651.906| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.85 r_work: 0.3069 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8934 Z= 0.118 Angle : 0.558 10.357 12111 Z= 0.293 Chirality : 0.044 0.163 1397 Planarity : 0.004 0.052 1523 Dihedral : 6.766 178.540 1221 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.07 % Allowed : 20.26 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1101 helix: -0.44 (0.28), residues: 373 sheet: 0.59 (0.30), residues: 279 loop : -0.76 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.023 0.001 TYR R 268 PHE 0.015 0.001 PHE B 216 TRP 0.010 0.001 TRP S 47 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8927) covalent geometry : angle 0.55775 / 0.29 (12097) SS BOND : bond 0.00621 / 0.31 ( 4) SS BOND : angle 0.68893 / 0.40 ( 8) hydrogen bonds : bond 0.03998 / 2.63 ( 311) hydrogen bonds : angle 4.21945 / 2.95 ( 888) Misc. bond : bond 0.00047 / 0.02 ( 1) link_TRANS : bond 0.00105 / 0.05 ( 2) link_TRANS : angle 0.56837 / 0.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.57 seconds wall clock time: 50 minutes 14.80 seconds (3014.80 seconds total)