Starting phenix.real_space_refine on Tue Mar 3 21:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aue_11927/03_2026/7aue_11927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aue_11927/03_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_11927/03_2026/7aue_11927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_2026/7aue_11927.map" model { file = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_2026/7aue_11927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_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-5986/lib/python3.9/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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} 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: 2.24, per 1000 atoms: 0.26 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: 0.57 Conformation dependent library (CDL) restraints added in 249.1 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: 0.31 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: 1.35 Time building geometry restraints manager: 0.79 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: 5231 35.97 - 71.95: 64 71.95 - 107.92: 6 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 5302 sinusoidal: 2021 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 5299 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: 1.490 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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= 0.424 Angle : 0.805 11.384 12111 Z= 0.450 Chirality : 0.052 0.272 1397 Planarity : 0.006 0.066 1523 Dihedral : 14.183 179.865 3162 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 covalent geometry : bond 0.00608 ( 8927) covalent geometry : angle 0.80275 (12097) SS BOND : bond 0.00492 ( 4) SS BOND : angle 1.06597 ( 8) hydrogen bonds : bond 0.32177 ( 311) hydrogen bonds : angle 9.81489 ( 888) Misc. bond : bond 0.09497 ( 1) link_TRANS : bond 0.12946 ( 2) link_TRANS : angle 2.54486 ( 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 : 0.369 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: 0.6410 time to fit residues: 117.1084 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 : 0.337 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3608 r_free = 0.3608 target = 0.138024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107556 restraints weight = 10817.903| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.99 r_work: 0.3085 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1749 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= 0.100 Angle : 0.548 9.758 12111 Z= 0.295 Chirality : 0.043 0.197 1397 Planarity : 0.004 0.044 1523 Dihedral : 7.295 178.902 1226 Min Nonbonded Distance : 2.305 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: -3.23 (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 C 2 TYR 0.026 0.001 TYR A 297 PHE 0.013 0.001 PHE B 216 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8927) covalent geometry : angle 0.54844 (12097) SS BOND : bond 0.00393 ( 4) SS BOND : angle 0.68901 ( 8) hydrogen bonds : bond 0.04847 ( 311) hydrogen bonds : angle 5.26113 ( 888) Misc. bond : bond 0.00047 ( 1) link_TRANS : bond 0.00171 ( 2) link_TRANS : angle 0.42999 ( 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 156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.213 Fit side-chains REVERT: R 200 MET cc_start: 0.7721 (mtt) cc_final: 0.7331 (mtt) REVERT: R 204 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6852 (mpp) REVERT: R 215 MET cc_start: 0.8625 (mtp) cc_final: 0.8419 (mtp) REVERT: R 242 LYS cc_start: 0.8063 (tttp) cc_final: 0.7664 (tttm) REVERT: R 281 MET cc_start: 0.7356 (mtm) cc_final: 0.6950 (mtt) REVERT: R 310 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7500 (ttp80) REVERT: R 311 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7357 (mttt) REVERT: A 24 ARG cc_start: 0.7211 (mtt-85) cc_final: 0.6735 (mtm110) REVERT: A 199 HIS cc_start: 0.7616 (t-90) cc_final: 0.7055 (t-170) REVERT: A 234 MET cc_start: 0.7217 (mtp) cc_final: 0.6916 (mtt) REVERT: A 301 GLU cc_start: 0.5514 (pm20) cc_final: 0.4971 (tm-30) REVERT: A 351 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7121 (pp) REVERT: B 37 ASP cc_start: 0.7720 (m-30) cc_final: 0.7462 (m-30) REVERT: B 93 ASP cc_start: 0.8018 (p0) cc_final: 0.7680 (p0) REVERT: B 118 MET cc_start: 0.9003 (mtp) cc_final: 0.8632 (mtm) REVERT: G 42 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7490 (tm-30) REVERT: G 47 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7445 (tt0) REVERT: S 93 MET cc_start: 0.8386 (ttm) cc_final: 0.8090 (ttt) outliers start: 13 outliers final: 0 residues processed: 150 average time/residue: 0.6843 time to fit residues: 107.8127 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 : 0.211 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS R 307 GLN A 250 ASN B 254 ASN 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 = 0.3549 r_free = 0.3549 target = 0.133365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102309 restraints weight = 10849.307| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.82 r_work: 0.2983 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8934 Z= 0.218 Angle : 0.693 10.275 12111 Z= 0.369 Chirality : 0.049 0.236 1397 Planarity : 0.005 0.039 1523 Dihedral : 7.365 177.095 1222 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.67 % Allowed : 14.82 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.40 (0.23), residues: 1101 helix: -2.49 (0.23), residues: 378 sheet: -0.05 (0.31), residues: 279 loop : -1.61 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 214 TYR 0.031 0.002 TYR A 297 PHE 0.019 0.002 PHE A 355 TRP 0.014 0.002 TRP S 47 HIS 0.006 0.001 HIS R 214 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8927) covalent geometry : angle 0.69246 (12097) SS BOND : bond 0.00988 ( 4) SS BOND : angle 1.17212 ( 8) hydrogen bonds : bond 0.06280 ( 311) hydrogen bonds : angle 5.27647 ( 888) Misc. bond : bond 0.00095 ( 1) link_TRANS : bond 0.00137 ( 2) link_TRANS : angle 0.89568 ( 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 156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.271 Fit side-chains REVERT: R 204 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7062 (mpp) REVERT: R 215 MET cc_start: 0.8621 (mtp) cc_final: 0.8417 (mtp) REVERT: R 242 LYS cc_start: 0.8166 (tttp) cc_final: 0.7760 (tttm) REVERT: R 281 MET cc_start: 0.7450 (mtm) cc_final: 0.7141 (mtt) REVERT: R 310 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7579 (ttp80) REVERT: R 311 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7395 (mttt) REVERT: A 24 ARG cc_start: 0.7584 (mtt-85) cc_final: 0.7197 (mtm-85) REVERT: A 301 GLU cc_start: 0.5691 (pm20) cc_final: 0.5125 (pp20) REVERT: A 348 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7597 (t) REVERT: B 37 ASP cc_start: 0.7682 (m-30) cc_final: 0.7463 (m-30) REVERT: B 93 ASP cc_start: 0.8204 (p0) cc_final: 0.7844 (p0) REVERT: B 118 MET cc_start: 0.9015 (mtp) cc_final: 0.8637 (mtm) REVERT: G 47 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7498 (tt0) REVERT: S 93 MET cc_start: 0.8552 (ttm) cc_final: 0.8291 (ttt) REVERT: S 196 SER cc_start: 0.8003 (p) cc_final: 0.7790 (m) outliers start: 25 outliers final: 6 residues processed: 143 average time/residue: 0.6509 time to fit residues: 98.2962 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 348 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 31 SER 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: 6.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 254 ASN S 13 GLN 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 = 0.3599 r_free = 0.3599 target = 0.137586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107321 restraints weight = 10862.186| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.75 r_work: 0.3013 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8934 Z= 0.148 Angle : 0.605 10.360 12111 Z= 0.322 Chirality : 0.046 0.190 1397 Planarity : 0.004 0.035 1523 Dihedral : 7.181 178.444 1222 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.67 % Allowed : 15.67 % Favored : 81.66 % 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: -1.90 (0.24), residues: 1101 helix: -1.92 (0.25), residues: 371 sheet: 0.13 (0.31), residues: 279 loop : -1.42 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.022 0.002 TYR A 297 PHE 0.017 0.002 PHE B 216 TRP 0.012 0.001 TRP S 47 HIS 0.006 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8927) covalent geometry : angle 0.60485 (12097) SS BOND : bond 0.00796 ( 4) SS BOND : angle 1.00019 ( 8) hydrogen bonds : bond 0.05066 ( 311) hydrogen bonds : angle 4.88692 ( 888) Misc. bond : bond 0.00074 ( 1) link_TRANS : bond 0.00103 ( 2) link_TRANS : angle 0.60086 ( 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 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.350 Fit side-chains REVERT: R 204 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7016 (mpp) REVERT: R 215 MET cc_start: 0.8643 (mtp) cc_final: 0.8436 (mtp) REVERT: R 242 LYS cc_start: 0.8113 (tttp) cc_final: 0.7683 (tttm) REVERT: R 281 MET cc_start: 0.7434 (mtm) cc_final: 0.7123 (mtt) REVERT: R 310 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7475 (ttp80) REVERT: R 311 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7400 (mttt) REVERT: A 24 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.6856 (mtm110) REVERT: A 297 TYR cc_start: 0.5837 (t80) cc_final: 0.5595 (t80) REVERT: A 301 GLU cc_start: 0.5612 (pm20) cc_final: 0.5058 (pp20) REVERT: A 336 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8578 (p-80) REVERT: B 37 ASP cc_start: 0.7642 (m-30) cc_final: 0.7417 (m-30) REVERT: B 93 ASP cc_start: 0.8169 (p0) cc_final: 0.7817 (p0) REVERT: B 118 MET cc_start: 0.8995 (mtp) cc_final: 0.8615 (mtm) REVERT: G 42 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7657 (tm-30) REVERT: G 47 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7461 (tt0) REVERT: S 65 LYS cc_start: 0.7627 (tptt) cc_final: 0.7317 (tttp) REVERT: S 93 MET cc_start: 0.8519 (ttm) cc_final: 0.8245 (ttt) REVERT: S 196 SER cc_start: 0.7920 (p) cc_final: 0.7706 (m) outliers start: 25 outliers final: 7 residues processed: 145 average time/residue: 0.6769 time to fit residues: 103.5433 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER 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: 3.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 254 ASN S 13 GLN 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 = 0.3586 r_free = 0.3586 target = 0.136401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105975 restraints weight = 10791.360| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.90 r_work: 0.3037 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8934 Z= 0.136 Angle : 0.589 10.314 12111 Z= 0.312 Chirality : 0.045 0.187 1397 Planarity : 0.004 0.038 1523 Dihedral : 7.072 178.633 1222 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.56 % Allowed : 16.31 % Favored : 81.13 % 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: -1.59 (0.25), residues: 1101 helix: -1.58 (0.26), residues: 371 sheet: 0.23 (0.31), residues: 279 loop : -1.28 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.021 0.002 TYR A 297 PHE 0.017 0.002 PHE B 216 TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8927) covalent geometry : angle 0.58834 (12097) SS BOND : bond 0.00756 ( 4) SS BOND : angle 0.95121 ( 8) hydrogen bonds : bond 0.04735 ( 311) hydrogen bonds : angle 4.65130 ( 888) Misc. bond : bond 0.00072 ( 1) link_TRANS : bond 0.00095 ( 2) link_TRANS : angle 0.57547 ( 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 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.355 Fit side-chains REVERT: R 46 VAL cc_start: 0.8494 (p) cc_final: 0.8208 (t) REVERT: R 204 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6968 (mpp) REVERT: R 215 MET cc_start: 0.8637 (mtp) cc_final: 0.8423 (mtp) REVERT: R 242 LYS cc_start: 0.8136 (tttp) cc_final: 0.7828 (tttm) REVERT: R 281 MET cc_start: 0.7380 (mtm) cc_final: 0.7061 (mtt) REVERT: R 310 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7462 (ttp-170) REVERT: R 311 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7400 (mttt) REVERT: A 24 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.6819 (mtm110) REVERT: A 259 ARG cc_start: 0.7810 (ptt90) cc_final: 0.7420 (ptt90) REVERT: A 288 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5570 (tp30) REVERT: A 301 GLU cc_start: 0.5639 (pm20) cc_final: 0.5010 (pp20) REVERT: A 336 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8576 (p-80) REVERT: B 29 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6467 (tp30) REVERT: B 37 ASP cc_start: 0.7584 (m-30) cc_final: 0.7325 (m-30) REVERT: B 118 MET cc_start: 0.8985 (mtp) cc_final: 0.8602 (mtm) REVERT: G 22 GLU cc_start: 0.7159 (tt0) cc_final: 0.6406 (mt-10) REVERT: G 42 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7646 (tm-30) REVERT: G 47 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7460 (tt0) REVERT: S 65 LYS cc_start: 0.7602 (tptt) cc_final: 0.7304 (tttp) REVERT: S 93 MET cc_start: 0.8487 (ttm) cc_final: 0.8205 (ttt) REVERT: S 207 LEU cc_start: 0.7139 (mp) cc_final: 0.6783 (pt) outliers start: 24 outliers final: 12 residues processed: 148 average time/residue: 0.6124 time to fit residues: 95.9758 Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 197 LEU 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 263 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 150 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 254 ASN S 13 GLN 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 = 0.3574 r_free = 0.3574 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104925 restraints weight = 10874.679| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.75 r_work: 0.3012 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8934 Z= 0.146 Angle : 0.602 10.212 12111 Z= 0.318 Chirality : 0.046 0.173 1397 Planarity : 0.004 0.040 1523 Dihedral : 7.072 178.292 1222 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.88 % Allowed : 16.52 % Favored : 80.60 % 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: -1.46 (0.25), residues: 1101 helix: -1.45 (0.26), residues: 373 sheet: 0.29 (0.31), residues: 279 loop : -1.21 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.019 0.002 TYR R 268 PHE 0.017 0.002 PHE B 216 TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8927) covalent geometry : angle 0.60145 (12097) SS BOND : bond 0.00779 ( 4) SS BOND : angle 0.97902 ( 8) hydrogen bonds : bond 0.04837 ( 311) hydrogen bonds : angle 4.61731 ( 888) Misc. bond : bond 0.00070 ( 1) link_TRANS : bond 0.00091 ( 2) link_TRANS : angle 0.57269 ( 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 160 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.316 Fit side-chains REVERT: R 46 VAL cc_start: 0.8500 (p) cc_final: 0.8222 (t) REVERT: R 204 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7022 (mpp) REVERT: R 215 MET cc_start: 0.8646 (mtp) cc_final: 0.8439 (mtp) REVERT: R 242 LYS cc_start: 0.8155 (tttp) cc_final: 0.7669 (tttm) REVERT: R 281 MET cc_start: 0.7450 (mtm) cc_final: 0.7140 (mtt) REVERT: R 310 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7481 (ttp-170) REVERT: R 311 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7383 (mttt) REVERT: A 24 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.6868 (mtm110) REVERT: A 232 TYR cc_start: 0.7841 (p90) cc_final: 0.7618 (p90) REVERT: A 259 ARG cc_start: 0.7865 (ptt90) cc_final: 0.7419 (ptt90) REVERT: A 297 TYR cc_start: 0.5687 (t80) cc_final: 0.5446 (t80) REVERT: A 301 GLU cc_start: 0.5635 (pm20) cc_final: 0.4987 (pp20) REVERT: A 336 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (p-80) REVERT: B 29 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6538 (tp30) REVERT: B 118 MET cc_start: 0.8990 (mtp) cc_final: 0.8611 (mtm) REVERT: B 290 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8575 (mp) REVERT: G 22 GLU cc_start: 0.7119 (tt0) cc_final: 0.6502 (mt-10) REVERT: G 42 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7668 (tm-30) REVERT: G 47 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7536 (tt0) REVERT: S 65 LYS cc_start: 0.7631 (tptt) cc_final: 0.7310 (tttp) REVERT: S 93 MET cc_start: 0.8521 (ttm) cc_final: 0.8242 (ttt) REVERT: S 207 LEU cc_start: 0.7292 (mp) cc_final: 0.6828 (pt) REVERT: C 2 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.3038 (tpm170) outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 0.6346 time to fit residues: 100.6644 Evaluate side-chains 153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 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 Chi-restraints excluded: chain S residue 150 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: 1.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 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 = 0.3618 r_free = 0.3618 target = 0.139252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108722 restraints weight = 10676.527| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.85 r_work: 0.3055 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2314 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= 0.109 Angle : 0.550 10.242 12111 Z= 0.289 Chirality : 0.044 0.162 1397 Planarity : 0.003 0.047 1523 Dihedral : 6.877 179.177 1222 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 17.59 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.16 (0.25), residues: 1101 helix: -1.09 (0.27), residues: 372 sheet: 0.35 (0.31), residues: 280 loop : -1.08 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.021 0.001 TYR R 268 PHE 0.015 0.001 PHE B 216 TRP 0.010 0.001 TRP B 228 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8927) covalent geometry : angle 0.54968 (12097) SS BOND : bond 0.00599 ( 4) SS BOND : angle 0.74789 ( 8) hydrogen bonds : bond 0.04038 ( 311) hydrogen bonds : angle 4.32873 ( 888) Misc. bond : bond 0.00048 ( 1) link_TRANS : bond 0.00114 ( 2) link_TRANS : angle 0.55215 ( 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 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.240 Fit side-chains REVERT: R 46 VAL cc_start: 0.8475 (p) cc_final: 0.8254 (t) REVERT: R 204 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.6978 (mpp) REVERT: R 242 LYS cc_start: 0.8156 (tttp) cc_final: 0.7829 (tttm) REVERT: R 281 MET cc_start: 0.7415 (mtm) cc_final: 0.7042 (mtt) REVERT: R 310 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7424 (ttp-170) REVERT: R 311 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7408 (mttt) REVERT: A 24 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7104 (mtm-85) REVERT: A 234 MET cc_start: 0.7279 (mtp) cc_final: 0.6992 (mtt) REVERT: A 259 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7420 (ptt90) REVERT: A 297 TYR cc_start: 0.5620 (t80) cc_final: 0.5409 (t80) REVERT: A 301 GLU cc_start: 0.5473 (pm20) cc_final: 0.4866 (pp20) REVERT: A 336 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (p-80) REVERT: B 29 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6574 (tp30) REVERT: B 118 MET cc_start: 0.8998 (mtp) cc_final: 0.8627 (mtm) REVERT: B 290 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8577 (mp) REVERT: G 22 GLU cc_start: 0.7105 (tt0) cc_final: 0.6459 (mt-10) REVERT: G 42 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7656 (tm-30) REVERT: G 47 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7445 (tt0) REVERT: S 65 LYS cc_start: 0.7576 (tptt) cc_final: 0.7271 (tttp) REVERT: S 93 MET cc_start: 0.8488 (ttm) cc_final: 0.8198 (ttt) REVERT: S 207 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6869 (pt) REVERT: C 2 ARG cc_start: 0.4780 (OUTLIER) cc_final: 0.3073 (tpm170) outliers start: 23 outliers final: 9 residues processed: 148 average time/residue: 0.6429 time to fit residues: 100.3395 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain G residue 46 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 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 = 0.3595 r_free = 0.3595 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106908 restraints weight = 10705.168| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.84 r_work: 0.3045 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 8934 Z= 0.123 Angle : 0.570 10.288 12111 Z= 0.301 Chirality : 0.044 0.167 1397 Planarity : 0.004 0.047 1523 Dihedral : 6.888 178.798 1222 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.13 % Allowed : 18.87 % 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: -1.03 (0.25), residues: 1101 helix: -0.92 (0.27), residues: 372 sheet: 0.39 (0.31), residues: 279 loop : -1.02 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.022 0.001 TYR R 268 PHE 0.016 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 covalent geometry : bond 0.00293 ( 8927) covalent geometry : angle 0.56987 (12097) SS BOND : bond 0.00652 ( 4) SS BOND : angle 0.83932 ( 8) hydrogen bonds : bond 0.04276 ( 311) hydrogen bonds : angle 4.36241 ( 888) Misc. bond : bond 0.00055 ( 1) link_TRANS : bond 0.00109 ( 2) link_TRANS : angle 0.57527 ( 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 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.330 Fit side-chains REVERT: R 46 VAL cc_start: 0.8501 (p) cc_final: 0.8282 (t) REVERT: R 204 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7042 (mpp) REVERT: R 242 LYS cc_start: 0.8192 (tttp) cc_final: 0.7860 (tttm) REVERT: R 281 MET cc_start: 0.7376 (mtm) cc_final: 0.7017 (mtt) REVERT: R 310 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7425 (ttp-170) REVERT: R 311 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7395 (mttt) REVERT: A 24 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7119 (mtm-85) REVERT: A 234 MET cc_start: 0.7296 (mtp) cc_final: 0.7004 (mtt) REVERT: A 259 ARG cc_start: 0.7798 (ptt90) cc_final: 0.7399 (ptt90) REVERT: A 301 GLU cc_start: 0.5508 (pm20) cc_final: 0.4894 (pp20) REVERT: A 336 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8585 (p-80) REVERT: B 29 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6610 (tp30) REVERT: B 118 MET cc_start: 0.8981 (mtp) cc_final: 0.8601 (mtm) REVERT: B 234 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7224 (pmm) REVERT: B 290 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8567 (mp) REVERT: G 22 GLU cc_start: 0.7102 (tt0) cc_final: 0.6501 (mt-10) REVERT: G 42 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7661 (tm-30) REVERT: G 47 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7480 (tt0) REVERT: S 65 LYS cc_start: 0.7597 (tptt) cc_final: 0.7281 (tttp) REVERT: S 93 MET cc_start: 0.8482 (ttm) cc_final: 0.8195 (ttt) REVERT: S 207 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6889 (pt) REVERT: C 2 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.3059 (tpm170) outliers start: 20 outliers final: 12 residues processed: 143 average time/residue: 0.6405 time to fit residues: 96.7121 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 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 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 28 optimal weight: 0.0030 chunk 29 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 overall best weight: 0.9892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN G 24 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 = 0.3609 r_free = 0.3609 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107930 restraints weight = 10740.954| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.87 r_work: 0.3061 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8934 Z= 0.104 Angle : 0.541 10.291 12111 Z= 0.285 Chirality : 0.043 0.146 1397 Planarity : 0.003 0.051 1523 Dihedral : 6.770 179.258 1222 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.92 % Allowed : 19.30 % Favored : 78.78 % 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: -0.81 (0.26), residues: 1101 helix: -0.67 (0.28), residues: 372 sheet: 0.45 (0.31), residues: 279 loop : -0.92 (0.30), residues: 450 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 0.009 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8927) covalent geometry : angle 0.54124 (12097) SS BOND : bond 0.00551 ( 4) SS BOND : angle 0.69197 ( 8) hydrogen bonds : bond 0.03798 ( 311) hydrogen bonds : angle 4.20095 ( 888) Misc. bond : bond 0.00044 ( 1) link_TRANS : bond 0.00112 ( 2) link_TRANS : angle 0.55344 ( 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 153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.341 Fit side-chains REVERT: R 242 LYS cc_start: 0.8181 (tttp) cc_final: 0.7687 (tttm) REVERT: R 281 MET cc_start: 0.7405 (mtm) cc_final: 0.7053 (mtt) REVERT: R 310 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7401 (ttp-170) REVERT: R 311 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7404 (mttt) REVERT: A 24 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.7134 (mtm-85) REVERT: A 199 HIS cc_start: 0.7645 (t-90) cc_final: 0.7339 (t-170) REVERT: A 234 MET cc_start: 0.7253 (mtp) cc_final: 0.6954 (mtt) REVERT: A 259 ARG cc_start: 0.7788 (ptt90) cc_final: 0.7386 (ptt90) REVERT: A 297 TYR cc_start: 0.5360 (t80) cc_final: 0.5124 (t80) REVERT: A 301 GLU cc_start: 0.5494 (pm20) cc_final: 0.4941 (pp20) REVERT: A 336 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8571 (p-80) REVERT: B 29 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6649 (tp30) REVERT: B 118 MET cc_start: 0.8984 (mtp) cc_final: 0.8614 (mtm) REVERT: B 214 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7328 (mtp85) REVERT: G 22 GLU cc_start: 0.7079 (tt0) cc_final: 0.6457 (mt-10) REVERT: G 42 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7649 (tm-30) REVERT: G 47 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7422 (tt0) REVERT: S 65 LYS cc_start: 0.7581 (tptt) cc_final: 0.7251 (tttp) REVERT: S 93 MET cc_start: 0.8476 (ttm) cc_final: 0.8179 (ttt) REVERT: C 2 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.2997 (tpm170) outliers start: 18 outliers final: 9 residues processed: 147 average time/residue: 0.6358 time to fit residues: 98.8150 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 251 PHE 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 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: 8.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 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 = 0.3600 r_free = 0.3600 target = 0.137899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107029 restraints weight = 10746.914| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.83 r_work: 0.3049 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 8934 Z= 0.111 Angle : 0.547 10.312 12111 Z= 0.287 Chirality : 0.044 0.150 1397 Planarity : 0.003 0.048 1523 Dihedral : 6.762 179.053 1222 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.39 % Allowed : 20.36 % Favored : 78.25 % 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: -0.66 (0.26), residues: 1101 helix: -0.52 (0.28), residues: 372 sheet: 0.50 (0.30), residues: 279 loop : -0.84 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.024 0.001 TYR R 268 PHE 0.015 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 covalent geometry : bond 0.00266 ( 8927) covalent geometry : angle 0.54664 (12097) SS BOND : bond 0.00588 ( 4) SS BOND : angle 0.73219 ( 8) hydrogen bonds : bond 0.03945 ( 311) hydrogen bonds : angle 4.22727 ( 888) Misc. bond : bond 0.00049 ( 1) link_TRANS : bond 0.00114 ( 2) link_TRANS : angle 0.57492 ( 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: 13 poor density : 131 time to evaluate : 0.310 Fit side-chains REVERT: R 242 LYS cc_start: 0.8196 (tttp) cc_final: 0.7711 (tttm) REVERT: R 281 MET cc_start: 0.7462 (mtm) cc_final: 0.7112 (mtt) REVERT: R 310 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7423 (ttp-170) REVERT: R 311 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7415 (mttt) REVERT: A 24 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.7148 (mtm-85) REVERT: A 199 HIS cc_start: 0.7709 (t-90) cc_final: 0.7372 (t-170) REVERT: A 234 MET cc_start: 0.7290 (mtp) cc_final: 0.7025 (mtt) REVERT: A 259 ARG cc_start: 0.7841 (ptt90) cc_final: 0.7431 (ptt90) REVERT: A 293 GLU cc_start: 0.8155 (tp30) cc_final: 0.7847 (mm-30) REVERT: A 301 GLU cc_start: 0.5514 (pm20) cc_final: 0.4958 (pp20) REVERT: A 336 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8559 (p-80) REVERT: B 118 MET cc_start: 0.8988 (mtp) cc_final: 0.8612 (mtm) REVERT: B 214 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7346 (mtp85) REVERT: G 22 GLU cc_start: 0.7105 (tt0) cc_final: 0.6456 (mt-10) REVERT: G 42 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7667 (tm-30) REVERT: G 47 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7443 (tt0) REVERT: S 65 LYS cc_start: 0.7579 (tptt) cc_final: 0.7241 (tttp) REVERT: S 93 MET cc_start: 0.8505 (ttm) cc_final: 0.8208 (ttt) REVERT: S 207 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6138 (pp) REVERT: C 2 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.2931 (tpm170) outliers start: 13 outliers final: 12 residues processed: 141 average time/residue: 0.6924 time to fit residues: 102.7445 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 : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 251 PHE 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 Chi-restraints excluded: chain S residue 154 LEU 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 89 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 107 optimal weight: 0.0270 chunk 99 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN G 24 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 = 0.3643 r_free = 0.3643 target = 0.141728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111467 restraints weight = 10634.613| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.81 r_work: 0.3160 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.109 8934 Z= 0.090 Angle : 0.507 10.325 12111 Z= 0.265 Chirality : 0.042 0.138 1397 Planarity : 0.003 0.050 1523 Dihedral : 6.577 179.773 1222 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.17 % Allowed : 20.58 % Favored : 78.25 % 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: -0.49 (0.26), residues: 1101 helix: -0.36 (0.28), residues: 384 sheet: 0.64 (0.31), residues: 273 loop : -0.78 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.024 0.001 TYR R 268 PHE 0.013 0.001 PHE B 216 TRP 0.009 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8927) covalent geometry : angle 0.50679 (12097) SS BOND : bond 0.00436 ( 4) SS BOND : angle 0.59241 ( 8) hydrogen bonds : bond 0.03168 ( 311) hydrogen bonds : angle 3.97235 ( 888) Misc. bond : bond 0.00029 ( 1) link_TRANS : bond 0.00122 ( 2) link_TRANS : angle 0.55010 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.67 seconds wall clock time: 61 minutes 57.78 seconds (3717.78 seconds total)