Starting phenix.real_space_refine on Thu Mar 13 11:12:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aue_11927/03_2025/7aue_11927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aue_11927/03_2025/7aue_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_2025/7aue_11927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_2025/7aue_11927.map" model { file = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_2025/7aue_11927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aue_11927/03_2025/7aue_11927.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'ARG:plan': 2, 'ASP: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: 5.46, per 1000 atoms: 0.62 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: 2.25 Conformation dependent library (CDL) restraints added in 990.9 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: 1.07 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: 2.24 Time building geometry restraints manager: 2.57 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: 1.370 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- 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 8927 Z= 0.408 Angle : 0.803 11.384 12097 Z= 0.449 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 : 1.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 228 HIS 0.011 0.002 HIS R 264 PHE 0.022 0.002 PHE B 216 TYR 0.028 0.002 TYR A 297 ARG 0.005 0.000 ARG B 268 *********************** 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 : 1.077 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: 1.4449 time to fit residues: 264.8055 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 : 1.365 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.0040 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 108 HIS B 254 ASN S 13 GLN S 113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108063 restraints weight = 10783.215| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.99 r_work: 0.3091 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8927 Z= 0.134 Angle : 0.545 9.366 12097 Z= 0.293 Chirality : 0.043 0.195 1397 Planarity : 0.004 0.044 1523 Dihedral : 7.268 178.786 1226 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.28 % Allowed : 13.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.22), residues: 1101 helix: -3.24 (0.19), residues: 375 sheet: -0.54 (0.30), residues: 273 loop : -1.69 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS R 264 PHE 0.013 0.001 PHE B 216 TYR 0.026 0.001 TYR A 297 ARG 0.002 0.000 ARG G 13 *********************** 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 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.037 Fit side-chains REVERT: R 200 MET cc_start: 0.7709 (mtt) cc_final: 0.7321 (mtt) REVERT: R 204 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.6844 (mpp) REVERT: R 242 LYS cc_start: 0.8054 (tttp) cc_final: 0.7652 (tttm) REVERT: R 281 MET cc_start: 0.7361 (mtm) cc_final: 0.6946 (mtt) REVERT: R 310 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7497 (ttp80) REVERT: R 311 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7362 (mttt) REVERT: A 24 ARG cc_start: 0.7200 (mtt-85) cc_final: 0.6727 (mtm110) REVERT: A 199 HIS cc_start: 0.7621 (t-90) cc_final: 0.7069 (t-170) REVERT: A 234 MET cc_start: 0.7222 (mtp) cc_final: 0.6925 (mtt) REVERT: A 301 GLU cc_start: 0.5504 (pm20) cc_final: 0.5010 (tm-30) REVERT: A 351 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7126 (pp) REVERT: B 37 ASP cc_start: 0.7628 (m-30) cc_final: 0.7378 (m-30) REVERT: B 93 ASP cc_start: 0.8064 (p0) cc_final: 0.7710 (p0) REVERT: B 118 MET cc_start: 0.8999 (mtp) cc_final: 0.8629 (mtm) REVERT: G 42 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7496 (tm-30) REVERT: G 47 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7449 (tt0) REVERT: S 93 MET cc_start: 0.8377 (ttm) cc_final: 0.8076 (ttt) outliers start: 12 outliers final: 1 residues processed: 154 average time/residue: 1.8064 time to fit residues: 292.9725 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.0010 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.8668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 105 ASN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107700 restraints weight = 10871.354| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.79 r_work: 0.3066 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8927 Z= 0.137 Angle : 0.525 9.447 12097 Z= 0.279 Chirality : 0.043 0.190 1397 Planarity : 0.003 0.033 1523 Dihedral : 7.001 178.106 1226 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.81 % Allowed : 15.78 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1101 helix: -2.13 (0.24), residues: 375 sheet: -0.06 (0.31), residues: 275 loop : -1.48 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 PHE 0.013 0.001 PHE B 216 TYR 0.022 0.001 TYR A 297 ARG 0.004 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: R 46 VAL cc_start: 0.8357 (p) cc_final: 0.8114 (t) REVERT: R 200 MET cc_start: 0.7686 (mtt) cc_final: 0.7253 (mtt) REVERT: R 204 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.6927 (mpp) REVERT: R 242 LYS cc_start: 0.8084 (tttp) cc_final: 0.7723 (tttm) REVERT: R 281 MET cc_start: 0.7465 (mtm) cc_final: 0.7111 (mtt) REVERT: R 310 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7508 (ttp80) REVERT: R 311 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7441 (mttt) REVERT: A 24 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.6947 (mtm110) REVERT: A 199 HIS cc_start: 0.7662 (t-90) cc_final: 0.7160 (t-170) REVERT: A 234 MET cc_start: 0.7420 (mtp) cc_final: 0.7154 (mtt) REVERT: A 301 GLU cc_start: 0.5592 (pm20) cc_final: 0.5049 (tm-30) REVERT: B 37 ASP cc_start: 0.7791 (m-30) cc_final: 0.7532 (m-30) REVERT: B 118 MET cc_start: 0.8989 (mtp) cc_final: 0.8619 (mtm) REVERT: B 192 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: B 284 ASP cc_start: 0.7420 (m-30) cc_final: 0.7166 (m-30) REVERT: G 42 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7724 (tm-30) REVERT: G 47 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7489 (tt0) REVERT: S 93 MET cc_start: 0.8423 (ttm) cc_final: 0.8135 (ttt) outliers start: 17 outliers final: 4 residues processed: 140 average time/residue: 1.3967 time to fit residues: 206.7687 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 3 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.0010 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 274 ASN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106694 restraints weight = 10779.904| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.87 r_work: 0.3078 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 8927 Z= 0.158 Angle : 0.530 10.089 12097 Z= 0.280 Chirality : 0.043 0.184 1397 Planarity : 0.003 0.033 1523 Dihedral : 6.757 178.923 1222 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.24 % Allowed : 15.78 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.25), residues: 1101 helix: -1.47 (0.26), residues: 376 sheet: 0.15 (0.31), residues: 280 loop : -1.28 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 PHE 0.013 0.001 PHE B 216 TYR 0.021 0.001 TYR A 297 ARG 0.005 0.000 ARG B 214 *********************** 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 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.007 Fit side-chains REVERT: R 200 MET cc_start: 0.7619 (mtt) cc_final: 0.7011 (mtt) REVERT: R 204 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.6904 (mpp) REVERT: R 242 LYS cc_start: 0.8107 (tttp) cc_final: 0.7612 (tttm) REVERT: R 281 MET cc_start: 0.7435 (mtm) cc_final: 0.7072 (mtt) REVERT: R 310 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7369 (ttp80) REVERT: R 311 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7399 (mttt) REVERT: A 24 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.7055 (mtm-85) REVERT: A 234 MET cc_start: 0.7264 (mtp) cc_final: 0.6972 (mtt) REVERT: A 286 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7729 (tttt) REVERT: A 301 GLU cc_start: 0.5470 (pm20) cc_final: 0.4897 (pp20) REVERT: B 29 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6383 (tp30) REVERT: B 37 ASP cc_start: 0.7741 (m-30) cc_final: 0.7483 (m-30) REVERT: B 118 MET cc_start: 0.8977 (mtp) cc_final: 0.8600 (mtm) REVERT: B 192 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: G 42 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7695 (tm-30) REVERT: G 47 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7495 (tt0) REVERT: S 93 MET cc_start: 0.8395 (ttm) cc_final: 0.8077 (ttt) REVERT: S 128 MET cc_start: 0.8489 (mmm) cc_final: 0.8151 (mmt) REVERT: S 207 LEU cc_start: 0.7035 (mp) cc_final: 0.6637 (pt) REVERT: C 2 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.2880 (tpm170) outliers start: 21 outliers final: 4 residues processed: 145 average time/residue: 1.4588 time to fit residues: 223.1647 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107140 restraints weight = 10703.818| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.87 r_work: 0.3076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 8927 Z= 0.151 Angle : 0.514 10.001 12097 Z= 0.271 Chirality : 0.043 0.152 1397 Planarity : 0.003 0.032 1523 Dihedral : 6.691 179.444 1222 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.92 % Allowed : 16.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1101 helix: -1.11 (0.27), residues: 376 sheet: 0.30 (0.31), residues: 280 loop : -1.14 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS R 264 PHE 0.013 0.001 PHE B 216 TYR 0.020 0.001 TYR R 268 ARG 0.006 0.000 ARG B 214 *********************** 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 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.923 Fit side-chains REVERT: R 204 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7059 (mpp) REVERT: R 242 LYS cc_start: 0.8132 (tttp) cc_final: 0.7627 (tttm) REVERT: R 281 MET cc_start: 0.7504 (mtm) cc_final: 0.7151 (mtt) REVERT: R 310 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7464 (ttp80) REVERT: R 311 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7454 (mttt) REVERT: A 199 HIS cc_start: 0.7628 (t-90) cc_final: 0.7015 (m170) REVERT: A 234 MET cc_start: 0.7201 (mtp) cc_final: 0.6924 (mtt) REVERT: A 288 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5552 (tp30) REVERT: A 297 TYR cc_start: 0.5355 (t80) cc_final: 0.5091 (t80) REVERT: A 301 GLU cc_start: 0.5530 (pm20) cc_final: 0.4978 (pp20) REVERT: B 29 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6475 (tp30) REVERT: B 118 MET cc_start: 0.8972 (mtp) cc_final: 0.8607 (mtm) REVERT: B 192 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: G 47 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7445 (tt0) REVERT: S 93 MET cc_start: 0.8440 (ttm) cc_final: 0.8145 (ttt) REVERT: S 128 MET cc_start: 0.8463 (mmm) cc_final: 0.8243 (mmt) REVERT: S 207 LEU cc_start: 0.7079 (mp) cc_final: 0.6764 (pt) REVERT: C 2 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.2854 (tpm170) outliers start: 18 outliers final: 4 residues processed: 142 average time/residue: 1.3805 time to fit residues: 207.3334 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS A 52 GLN B 254 ASN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102783 restraints weight = 10795.535| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.73 r_work: 0.2986 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8927 Z= 0.361 Angle : 0.688 10.053 12097 Z= 0.365 Chirality : 0.050 0.193 1397 Planarity : 0.004 0.041 1523 Dihedral : 7.208 176.808 1222 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.25), residues: 1101 helix: -1.48 (0.25), residues: 373 sheet: 0.36 (0.31), residues: 278 loop : -1.21 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.007 0.001 HIS R 214 PHE 0.020 0.002 PHE B 216 TYR 0.020 0.002 TYR A 297 ARG 0.005 0.001 ARG B 214 *********************** 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 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.246 Fit side-chains REVERT: R 204 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: R 242 LYS cc_start: 0.8104 (tttp) cc_final: 0.7713 (tttm) REVERT: R 281 MET cc_start: 0.7457 (mtm) cc_final: 0.7155 (mtt) REVERT: R 310 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7486 (ttp-170) REVERT: R 311 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7418 (mttt) REVERT: A 24 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7081 (ttm110) REVERT: A 288 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5540 (tp30) REVERT: A 297 TYR cc_start: 0.5930 (t80) cc_final: 0.5663 (t80) REVERT: A 301 GLU cc_start: 0.5598 (pm20) cc_final: 0.4977 (pp20) REVERT: B 29 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6545 (tp30) REVERT: B 118 MET cc_start: 0.9012 (mtp) cc_final: 0.8645 (mtm) REVERT: B 284 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: G 22 GLU cc_start: 0.7106 (tt0) cc_final: 0.6442 (mt-10) REVERT: G 47 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7589 (tt0) REVERT: S 93 MET cc_start: 0.8542 (ttm) cc_final: 0.8273 (ttt) REVERT: C 2 ARG cc_start: 0.5003 (OUTLIER) cc_final: 0.2957 (tpm170) outliers start: 22 outliers final: 6 residues processed: 141 average time/residue: 1.5029 time to fit residues: 223.7899 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 284 ASP 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 C residue 2 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN G 24 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105559 restraints weight = 10813.127| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.75 r_work: 0.3027 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 8927 Z= 0.201 Angle : 0.573 9.990 12097 Z= 0.304 Chirality : 0.045 0.174 1397 Planarity : 0.004 0.049 1523 Dihedral : 6.973 178.678 1222 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.71 % Allowed : 18.12 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1101 helix: -1.15 (0.26), residues: 373 sheet: 0.40 (0.31), residues: 279 loop : -1.10 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS A 199 PHE 0.016 0.001 PHE B 216 TYR 0.020 0.001 TYR R 268 ARG 0.012 0.000 ARG B 214 *********************** 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 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.092 Fit side-chains REVERT: R 204 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7093 (mpp) REVERT: R 242 LYS cc_start: 0.8137 (tttp) cc_final: 0.7730 (tttm) REVERT: R 281 MET cc_start: 0.7462 (mtm) cc_final: 0.7153 (mtt) REVERT: R 310 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7433 (ttp80) REVERT: R 311 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7336 (mttt) REVERT: A 24 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7135 (ttm110) REVERT: A 234 MET cc_start: 0.7289 (mtp) cc_final: 0.6966 (mtt) REVERT: A 301 GLU cc_start: 0.5557 (pm20) cc_final: 0.4980 (pp20) REVERT: A 353 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7351 (mtp180) REVERT: B 29 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6588 (tp30) REVERT: B 118 MET cc_start: 0.9016 (mtp) cc_final: 0.8642 (mtm) REVERT: G 22 GLU cc_start: 0.7112 (tt0) cc_final: 0.6387 (mt-10) REVERT: G 47 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7471 (tt0) REVERT: S 65 LYS cc_start: 0.7621 (tptt) cc_final: 0.7293 (tttp) REVERT: S 93 MET cc_start: 0.8478 (ttm) cc_final: 0.8187 (ttt) REVERT: S 207 LEU cc_start: 0.7054 (mp) cc_final: 0.6806 (pt) REVERT: C 2 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.2891 (tpm170) outliers start: 16 outliers final: 4 residues processed: 140 average time/residue: 1.4273 time to fit residues: 211.5669 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 353 ARG Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 67 optimal weight: 7.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107603 restraints weight = 10916.143| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.04 r_work: 0.3077 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 8927 Z= 0.157 Angle : 0.522 10.091 12097 Z= 0.275 Chirality : 0.043 0.144 1397 Planarity : 0.003 0.050 1523 Dihedral : 6.726 179.455 1222 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.71 % Allowed : 18.55 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1101 helix: -0.77 (0.27), residues: 377 sheet: 0.54 (0.31), residues: 278 loop : -1.01 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.005 0.001 HIS A 199 PHE 0.014 0.001 PHE B 216 TYR 0.022 0.001 TYR R 268 ARG 0.013 0.000 ARG B 214 *********************** 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.967 Fit side-chains REVERT: R 204 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7047 (mpp) REVERT: R 242 LYS cc_start: 0.8159 (tttp) cc_final: 0.7809 (tttm) REVERT: R 281 MET cc_start: 0.7460 (mtm) cc_final: 0.7087 (mtt) REVERT: R 310 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7288 (ttp80) REVERT: R 311 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7367 (mttt) REVERT: A 24 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7087 (ttm110) REVERT: A 234 MET cc_start: 0.7239 (mtp) cc_final: 0.6951 (mtt) REVERT: A 293 GLU cc_start: 0.8023 (tp30) cc_final: 0.7709 (mm-30) REVERT: A 297 TYR cc_start: 0.5434 (t80) cc_final: 0.5182 (t80) REVERT: A 301 GLU cc_start: 0.5520 (pm20) cc_final: 0.4926 (pp20) REVERT: A 353 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7297 (mtp180) REVERT: B 29 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6630 (tp30) REVERT: B 118 MET cc_start: 0.8998 (mtp) cc_final: 0.8635 (mtm) REVERT: B 214 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7331 (mtp85) REVERT: G 22 GLU cc_start: 0.7103 (tt0) cc_final: 0.6457 (mt-10) REVERT: G 47 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7405 (tt0) REVERT: S 65 LYS cc_start: 0.7548 (tptt) cc_final: 0.7200 (tttp) REVERT: S 93 MET cc_start: 0.8429 (ttm) cc_final: 0.8130 (ttt) REVERT: C 2 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.2805 (tpm170) outliers start: 16 outliers final: 7 residues processed: 143 average time/residue: 1.5810 time to fit residues: 238.8865 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 273 GLN B 254 ASN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108223 restraints weight = 10817.551| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.84 r_work: 0.3074 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 8927 Z= 0.172 Angle : 0.537 10.098 12097 Z= 0.284 Chirality : 0.043 0.150 1397 Planarity : 0.003 0.044 1523 Dihedral : 6.722 179.216 1222 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.39 % Allowed : 19.30 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1101 helix: -0.64 (0.28), residues: 378 sheet: 0.58 (0.31), residues: 279 loop : -0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.005 0.001 HIS A 199 PHE 0.015 0.001 PHE B 216 TYR 0.023 0.001 TYR R 268 ARG 0.011 0.000 ARG B 214 *********************** 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.965 Fit side-chains REVERT: R 204 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: R 242 LYS cc_start: 0.8140 (tttp) cc_final: 0.7658 (tttm) REVERT: R 281 MET cc_start: 0.7424 (mtm) cc_final: 0.7077 (mtt) REVERT: R 310 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7408 (ttp-170) REVERT: R 311 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7393 (mttt) REVERT: A 24 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7120 (ttm110) REVERT: A 234 MET cc_start: 0.7206 (mtp) cc_final: 0.6926 (mtt) REVERT: A 293 GLU cc_start: 0.8039 (tp30) cc_final: 0.7742 (mm-30) REVERT: A 297 TYR cc_start: 0.5495 (t80) cc_final: 0.5220 (t80) REVERT: A 301 GLU cc_start: 0.5532 (pm20) cc_final: 0.4933 (pp20) REVERT: B 29 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6565 (tp30) REVERT: B 118 MET cc_start: 0.8990 (mtp) cc_final: 0.8618 (mtm) REVERT: G 22 GLU cc_start: 0.7098 (tt0) cc_final: 0.6452 (mt-10) REVERT: G 47 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7442 (tt0) REVERT: S 65 LYS cc_start: 0.7557 (tptt) cc_final: 0.7228 (tttp) REVERT: S 93 MET cc_start: 0.8434 (ttm) cc_final: 0.8148 (ttt) REVERT: S 207 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6177 (pp) REVERT: C 2 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.2840 (tpm170) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 1.4552 time to fit residues: 213.2362 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 254 ASN G 24 ASN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109296 restraints weight = 10772.614| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.79 r_work: 0.3083 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 8927 Z= 0.165 Angle : 0.528 10.129 12097 Z= 0.278 Chirality : 0.043 0.149 1397 Planarity : 0.003 0.054 1523 Dihedral : 6.669 179.345 1222 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.39 % Allowed : 19.51 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1101 helix: -0.46 (0.28), residues: 378 sheet: 0.65 (0.31), residues: 280 loop : -0.86 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.005 0.001 HIS A 199 PHE 0.014 0.001 PHE B 216 TYR 0.024 0.001 TYR R 268 ARG 0.014 0.000 ARG B 214 ********************** 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 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.929 Fit side-chains REVERT: R 204 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7039 (mpp) REVERT: R 242 LYS cc_start: 0.8172 (tttp) cc_final: 0.7677 (tttm) REVERT: R 281 MET cc_start: 0.7420 (mtm) cc_final: 0.7088 (mtt) REVERT: R 310 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7400 (ttp-170) REVERT: R 311 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7390 (mttt) REVERT: A 24 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.6946 (ttm110) REVERT: A 234 MET cc_start: 0.7175 (mtp) cc_final: 0.6898 (mtt) REVERT: A 293 GLU cc_start: 0.8124 (tp30) cc_final: 0.7847 (mm-30) REVERT: A 297 TYR cc_start: 0.5629 (t80) cc_final: 0.5379 (t80) REVERT: A 301 GLU cc_start: 0.5499 (pm20) cc_final: 0.4923 (pp20) REVERT: B 118 MET cc_start: 0.8990 (mtp) cc_final: 0.8614 (mtm) REVERT: B 214 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7369 (mtp85) REVERT: G 22 GLU cc_start: 0.7070 (tt0) cc_final: 0.6480 (mt-10) REVERT: G 47 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7471 (tt0) REVERT: S 65 LYS cc_start: 0.7565 (tptt) cc_final: 0.7220 (tttp) REVERT: S 93 MET cc_start: 0.8413 (ttm) cc_final: 0.8133 (ttt) REVERT: C 2 ARG cc_start: 0.4717 (OUTLIER) cc_final: 0.2706 (tpm170) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 1.3931 time to fit residues: 207.3869 Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 52 optimal weight: 0.0010 chunk 105 optimal weight: 0.0040 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 254 ASN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113089 restraints weight = 10759.871| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.83 r_work: 0.3136 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 8927 Z= 0.143 Angle : 0.491 10.193 12097 Z= 0.256 Chirality : 0.042 0.144 1397 Planarity : 0.003 0.056 1523 Dihedral : 6.481 179.937 1222 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.85 % Allowed : 19.94 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1101 helix: -0.12 (0.29), residues: 377 sheet: 0.87 (0.32), residues: 268 loop : -0.74 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.004 0.001 HIS A 199 PHE 0.013 0.001 PHE R 267 TYR 0.023 0.001 TYR R 268 ARG 0.013 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7315.42 seconds wall clock time: 126 minutes 20.15 seconds (7580.15 seconds total)