Starting phenix.real_space_refine on Fri Oct 23 18:02:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.cif Found real_map, /net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25tx_80375/10_2026/25tx_80375.map" } resolution = 4.0 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6614 2.51 5 N 1813 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10500 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3851 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 26, 'TRANS': 500} Chain breaks: 2 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 12, 'ASN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 17, 'GLN:plan1': 7, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3776 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 22, 'TRANS': 476} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 995 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 3, 'TYR:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10500 At special positions: 0 Unit cell: (93.177, 119.952, 153.153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2016 8.00 N 1813 7.00 C 6614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 437 " distance=2.04 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 44 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 44 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " NAG E 1 " - " FUC E 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 4 " " NAG J 1 " - " FUC J 3 " NAG-ASN " NAG A1001 " - " ASN A 458 " " NAG A1002 " - " ASN A 98 " " NAG B1001 " - " ASN B 98 " " NAG D1201 " - " ASN D 122 " " NAG E 1 " - " ASN B 458 " " NAG F 1 " - " ASN C 59 " " NAG G 1 " - " ASN C 85 " " NAG H 1 " - " ASN C 90 " " NAG I 1 " - " ASN D 90 " " NAG J 1 " - " ASN D 59 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 378.2 milliseconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 14 sheets defined 31.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.756A pdb=" N ILE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.119A pdb=" N GLN A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.580A pdb=" N SER A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 removed outlier: 3.752A pdb=" N LEU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.726A pdb=" N ARG A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.734A pdb=" N LYS A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.661A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.564A pdb=" N PHE A 372 " --> pdb=" O TRP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.797A pdb=" N VAL A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 4.040A pdb=" N GLU A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 removed outlier: 4.225A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.418A pdb=" N GLY B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 75 through 92 removed outlier: 3.708A pdb=" N ALA B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.988A pdb=" N GLN B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.580A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.826A pdb=" N GLN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.915A pdb=" N GLU B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.855A pdb=" N ALA B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 246' Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.644A pdb=" N ASP B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.662A pdb=" N ALA B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 4.450A pdb=" N SER B 318 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.842A pdb=" N GLU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.542A pdb=" N ASP B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 407 through 430 removed outlier: 3.550A pdb=" N MET B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 removed outlier: 4.146A pdb=" N GLU B 441 " --> pdb=" O CYS B 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.919A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.197A pdb=" N GLY C 102 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.921A pdb=" N LEU C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 198 through 207 removed outlier: 3.690A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.694A pdb=" N ARG C 217 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.668A pdb=" N GLN C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.950A pdb=" N ARG D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.559A pdb=" N ALA A 103 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 49 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG A 104 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.559A pdb=" N ALA A 103 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY A 53 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 6.101A pdb=" N SER A 222 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 283 " --> pdb=" O VAL A 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 338 removed outlier: 4.452A pdb=" N ALA A 333 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 496 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN A 481 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 494 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.592A pdb=" N ILE B 105 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 49 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ARG B 104 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 106 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 53 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.499A pdb=" N VAL B 153 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 249 through 255 removed outlier: 7.122A pdb=" N VAL B 221 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER B 253 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR B 223 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG B 255 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 225 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 282 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.796A pdb=" N THR B 335 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 456 through 458 removed outlier: 3.606A pdb=" N PHE B 457 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 removed outlier: 4.106A pdb=" N ASP C 162 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.924A pdb=" N ALA D 42 " --> pdb=" O ARG D 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 251 hydrogen bonds defined for protein. 699 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: 1.31 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3470 1.35 - 1.47: 2500 1.47 - 1.58: 4653 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 10700 Sorted by residual: bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 10695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 14186 1.52 - 3.03: 299 3.03 - 4.55: 51 4.55 - 6.06: 17 6.06 - 7.58: 7 Bond angle restraints: 14560 Sorted by residual: angle pdb=" N VAL D 147 " pdb=" CA VAL D 147 " pdb=" C VAL D 147 " ideal model delta sigma weight residual 112.96 109.11 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" CA ASN C 90 " pdb=" CB ASN C 90 " pdb=" CG ASN C 90 " ideal model delta sigma weight residual 112.60 114.96 -2.36 1.00e+00 1.00e+00 5.55e+00 angle pdb=" CA MET B 466 " pdb=" CB MET B 466 " pdb=" CG MET B 466 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" CB MET B 466 " pdb=" CG MET B 466 " pdb=" SD MET B 466 " ideal model delta sigma weight residual 112.70 119.62 -6.92 3.00e+00 1.11e-01 5.32e+00 angle pdb=" N ASN D 90 " pdb=" CA ASN D 90 " pdb=" CB ASN D 90 " ideal model delta sigma weight residual 110.49 114.37 -3.88 1.69e+00 3.50e-01 5.26e+00 ... (remaining 14555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 6091 19.35 - 38.70: 440 38.70 - 58.04: 80 58.04 - 77.39: 30 77.39 - 96.74: 23 Dihedral angle restraints: 6664 sinusoidal: 2691 harmonic: 3973 Sorted by residual: dihedral pdb=" CB CYS A 249 " pdb=" SG CYS A 249 " pdb=" SG CYS A 541 " pdb=" CB CYS A 541 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS B 249 " pdb=" SG CYS B 249 " pdb=" SG CYS B 541 " pdb=" CB CYS B 541 " ideal model delta sinusoidal sigma weight residual 93.00 14.14 78.86 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS A 527 " pdb=" SG CYS A 527 " pdb=" SG CYS A 545 " pdb=" CB CYS A 545 " ideal model delta sinusoidal sigma weight residual -86.00 -124.23 38.23 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 6661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1711 0.161 - 0.321: 7 0.321 - 0.482: 0 0.482 - 0.642: 0 0.642 - 0.803: 1 Chirality restraints: 1719 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 90 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 458 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE C 168 " pdb=" CA ILE C 168 " pdb=" CG1 ILE C 168 " pdb=" CG2 ILE C 168 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1716 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " -0.005 2.00e-02 2.50e+03 2.94e-02 1.08e+01 pdb=" CG ASN D 90 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 48 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 49 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 568 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 569 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " -0.027 5.00e-02 4.00e+02 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2908 2.81 - 3.33: 10231 3.33 - 3.85: 16852 3.85 - 4.38: 19163 4.38 - 4.90: 32066 Nonbonded interactions: 81220 Sorted by model distance: nonbonded pdb=" NH2 ARG A 359 " pdb=" O ASP C 28 " model vdw 2.285 3.120 nonbonded pdb=" O PHE C 83 " pdb=" NE2 GLN C 107 " model vdw 2.320 3.120 nonbonded pdb=" O GLN B 118 " pdb=" OG1 THR B 121 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR A 50 " pdb=" O LYS A 149 " model vdw 2.325 3.040 nonbonded pdb=" NH2 ARG C 66 " pdb=" O7 NAG H 1 " model vdw 2.335 3.120 ... (remaining 81215 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 or (resid 48 and (name N or name CA or nam \ e C or name O or name CB )) or resid 49 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 145 or (resid 14 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 147 or (resi \ d 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thro \ ugh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) o \ r resid 174 through 258 or (resid 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 485 or (resid 486 through 489 and (name N or \ name CA or name C or name O or name CB )) or resid 490 through 524 or (resid 52 \ 5 and (name N or name CA or name C or name O or name CB )) or (resid 531 through \ 534 and (name N or name CA or name C or name O or name CB )) or resid 535 throu \ gh 536 or resid 541 through 546 or resid 1002)) selection = (chain 'B' and (resid 39 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 or (resid 94 and (name N or name CA or nam \ e C or name O or name CB )) or resid 95 through 128 or (resid 129 through 130 an \ d (name N or name CA or name C or name O or name CB )) or resid 131 through 132 \ or (resid 133 and (name N or name CA or name C or name O or name CB )) or resid \ 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) or re \ sid 136 through 188 or (resid 189 through 190 and (name N or name CA or name C o \ r name O or name CB )) or resid 191 through 226 or (resid 227 and (name N or nam \ e CA or name C or name O or name CB )) or resid 228 through 231 or (resid 232 th \ rough 233 and (name N or name CA or name C or name O or name CB )) or resid 234 \ through 235 or (resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 242 or (resid 243 through 245 and (name N or name CA or \ name C or name O or name CB )) or resid 246 through 247 or (resid 248 and (name \ N or name CA or name C or name O or name CB )) or resid 249 or (resid 250 throug \ h 252 and (name N or name CA or name C or name O or name CB )) or resid 253 thro \ ugh 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) o \ r resid 256 through 260 or (resid 261 and (name N or name CA or name C or name O \ or name CB )) or resid 262 through 288 or (resid 289 through 290 and (name N or \ name CA or name C or name O or name CB )) or resid 291 through 300 or (resid 30 \ 1 through 304 and (name N or name CA or name C or name O or name CB )) or resid \ 305 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 323 or (resid 324 through 328 and (name N or nam \ e CA or name C or name O or name CB )) or resid 329 through 330 or (resid 331 an \ d (name N or name CA or name C or name O or name CB )) or resid 332 through 343 \ or (resid 344 and (name N or name CA or name C or name O or name CB )) or resid \ 345 through 346 or (resid 347 through 348 and (name N or name CA or name C or na \ me O or name CB )) or resid 349 through 365 or (resid 366 and (name N or name CA \ or name C or name O or name CB )) or resid 367 through 374 or (resid 375 and (n \ ame N or name CA or name C or name O or name CB )) or resid 376 through 381 or ( \ resid 382 and (name N or name CA or name C or name O or name CB )) or resid 383 \ through 438 or (resid 439 and (name N or name CA or name C or name O or name CB \ )) or resid 440 through 441 or (resid 442 through 443 and (name N or name CA or \ name C or name O or name CB )) or resid 444 through 468 or (resid 469 and (name \ N or name CA or name C or name O or name CB )) or resid 470 through 487 or (resi \ d 488 through 489 and (name N or name CA or name C or name O or name CB )) or re \ sid 490 through 506 or (resid 507 and (name N or name CA or name C or name O or \ name CB )) or resid 508 through 517 or (resid 518 and (name N or name CA or name \ C or name O or name CB )) or resid 519 through 532 or (resid 533 through 534 an \ d (name N or name CA or name C or name O or name CB )) or resid 535 through 543 \ or (resid 544 and (name N or name CA or name C or name O or name CB )) or resid \ 545 through 1001)) } ncs_group { reference = (chain 'E' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } 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 group one per residue 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: 4.210 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.190 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.003 0.040 10736 Z= 0.141 Angle : 0.610 13.124 14652 Z= 0.275 Chirality : 0.048 0.803 1719 Planarity : 0.003 0.054 1874 Dihedral : 15.151 96.739 4060 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.23), residues: 1362 helix: 0.83 (0.30), residues: 330 sheet: -0.69 (0.46), residues: 138 loop : -1.51 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.009 0.001 TYR C 138 PHE 0.027 0.001 PHE A 122 TRP 0.011 0.001 TRP C 204 HIS 0.001 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (10700) covalent geometry : angle 0.55900 / 0.26 (14560) SS BOND : bond 0.00208 / 0.14 ( 16) SS BOND : angle 0.72671 / 0.53 ( 32) hydrogen bonds : bond 0.22750 / 15.90 ( 248) hydrogen bonds : angle 6.11037 / 4.26 ( 699) link_BETA1-4 : bond 0.00774 / 0.50 ( 7) link_BETA1-4 : angle 3.18451 / 2.10 ( 21) link_BETA1-6 : bond 0.00508 / 0.25 ( 3) link_BETA1-6 : angle 1.26545 / 0.70 ( 9) link_NAG-ASN : bond 0.00688 / 0.51 ( 10) link_NAG-ASN : angle 4.66181 / 3.12 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 ARG cc_start: 0.7113 (tpp80) cc_final: 0.6521 (mmm-85) REVERT: C 162 ASP cc_start: 0.8195 (p0) cc_final: 0.7812 (p0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0797 time to fit residues: 15.8421 Evaluate side-chains 100 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 107 GLN C 190 ASN C 219 GLN D 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.108606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.087210 restraints weight = 31411.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087763 restraints weight = 40620.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088382 restraints weight = 36112.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088925 restraints weight = 22115.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089756 restraints weight = 19349.298| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10736 Z= 0.299 Angle : 0.778 17.162 14652 Z= 0.381 Chirality : 0.053 0.890 1719 Planarity : 0.005 0.052 1874 Dihedral : 9.455 78.573 1882 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.27 % Allowed : 11.14 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.22), residues: 1362 helix: 0.36 (0.28), residues: 325 sheet: -1.40 (0.46), residues: 121 loop : -1.55 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 453 TYR 0.018 0.002 TYR A 477 PHE 0.019 0.002 PHE D 38 TRP 0.017 0.002 TRP A 363 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.30 (10700) covalent geometry : angle 0.73669 / 0.37 (14560) SS BOND : bond 0.00348 / 0.26 ( 16) SS BOND : angle 1.40783 / 1.01 ( 32) hydrogen bonds : bond 0.05130 / 3.73 ( 248) hydrogen bonds : angle 5.07804 / 3.62 ( 699) link_BETA1-4 : bond 0.00677 / 0.52 ( 7) link_BETA1-4 : angle 2.99365 / 2.44 ( 21) link_BETA1-6 : bond 0.00445 / 0.22 ( 3) link_BETA1-6 : angle 1.96619 / 1.02 ( 9) link_NAG-ASN : bond 0.00645 / 0.36 ( 10) link_NAG-ASN : angle 4.75032 / 3.36 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 162 ASP cc_start: 0.8418 (p0) cc_final: 0.8157 (p0) outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.0871 time to fit residues: 15.5293 Evaluate side-chains 104 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 30, 101, 46, 108, 79, 45, 105, 68, 134, 106] chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 134 optimal weight: 0.0040 chunk 106 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089455 restraints weight = 30921.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088746 restraints weight = 34200.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089470 restraints weight = 38172.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090419 restraints weight = 22774.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090807 restraints weight = 19791.401| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10736 Z= 0.115 Angle : 0.587 13.948 14652 Z= 0.282 Chirality : 0.046 0.613 1719 Planarity : 0.003 0.045 1874 Dihedral : 8.821 69.256 1882 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.47 % Allowed : 14.08 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.22), residues: 1362 helix: 0.67 (0.28), residues: 330 sheet: -0.84 (0.50), residues: 105 loop : -1.61 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.011 0.001 TYR D 138 PHE 0.027 0.001 PHE B 267 TRP 0.010 0.001 TRP D 40 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10700) covalent geometry : angle 0.54643 / 0.27 (14560) SS BOND : bond 0.00257 / 0.17 ( 16) SS BOND : angle 0.75660 / 0.59 ( 32) hydrogen bonds : bond 0.03704 / 2.67 ( 248) hydrogen bonds : angle 4.46763 / 3.16 ( 699) link_BETA1-4 : bond 0.00806 / 0.52 ( 7) link_BETA1-4 : angle 3.10487 / 2.42 ( 21) link_BETA1-6 : bond 0.00335 / 0.17 ( 3) link_BETA1-6 : angle 1.31245 / 0.70 ( 9) link_NAG-ASN : bond 0.00676 / 0.47 ( 10) link_NAG-ASN : angle 3.95720 / 2.81 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ASP cc_start: 0.8413 (p0) cc_final: 0.8122 (p0) outliers start: 15 outliers final: 7 residues processed: 113 average time/residue: 0.0818 time to fit residues: 14.3182 Evaluate side-chains 104 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 232 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [29, 106, 74, 66, 14, 48, 58, 72, 81, 113, 69] chunk 29 optimal weight: 0.0470 chunk 106 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 48 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089955 restraints weight = 30821.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089814 restraints weight = 36623.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090567 restraints weight = 36718.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.091523 restraints weight = 22950.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091864 restraints weight = 19782.439| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10736 Z= 0.110 Angle : 0.574 12.876 14652 Z= 0.273 Chirality : 0.045 0.575 1719 Planarity : 0.003 0.045 1874 Dihedral : 8.003 60.405 1882 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.76 % Allowed : 15.74 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.23), residues: 1362 helix: 0.84 (0.29), residues: 330 sheet: -0.78 (0.51), residues: 105 loop : -1.55 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.017 0.001 TYR D 136 PHE 0.011 0.001 PHE B 267 TRP 0.008 0.001 TRP B 310 HIS 0.002 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10700) covalent geometry : angle 0.53526 / 0.26 (14560) SS BOND : bond 0.00221 / 0.15 ( 16) SS BOND : angle 0.70627 / 0.55 ( 32) hydrogen bonds : bond 0.03147 / 2.27 ( 248) hydrogen bonds : angle 4.21795 / 2.98 ( 699) link_BETA1-4 : bond 0.00776 / 0.50 ( 7) link_BETA1-4 : angle 3.17382 / 2.52 ( 21) link_BETA1-6 : bond 0.00287 / 0.14 ( 3) link_BETA1-6 : angle 1.34121 / 0.71 ( 9) link_NAG-ASN : bond 0.00654 / 0.45 ( 10) link_NAG-ASN : angle 3.69099 / 2.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6228 (mp) REVERT: C 161 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8717 (pt) REVERT: C 162 ASP cc_start: 0.8441 (p0) cc_final: 0.8059 (p0) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.0788 time to fit residues: 14.5746 Evaluate side-chains 108 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [130, 26, 78, 39, 123, 133, 112, 105, 3, 2, 15] chunk 130 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.107798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086393 restraints weight = 31053.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088044 restraints weight = 37511.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088213 restraints weight = 31784.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088814 restraints weight = 19832.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089143 restraints weight = 18015.829| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10736 Z= 0.226 Angle : 0.673 13.983 14652 Z= 0.326 Chirality : 0.048 0.675 1719 Planarity : 0.004 0.050 1874 Dihedral : 7.211 58.442 1882 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.13 % Allowed : 16.13 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1362 helix: 0.66 (0.28), residues: 335 sheet: -1.36 (0.47), residues: 120 loop : -1.59 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 453 TYR 0.014 0.001 TYR A 179 PHE 0.012 0.001 PHE B 346 TRP 0.010 0.001 TRP A 316 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (10700) covalent geometry : angle 0.63696 / 0.32 (14560) SS BOND : bond 0.00337 / 0.23 ( 16) SS BOND : angle 0.93568 / 0.69 ( 32) hydrogen bonds : bond 0.03989 / 2.90 ( 248) hydrogen bonds : angle 4.49087 / 3.16 ( 699) link_BETA1-4 : bond 0.00700 / 0.51 ( 7) link_BETA1-4 : angle 3.13066 / 2.48 ( 21) link_BETA1-6 : bond 0.00294 / 0.15 ( 3) link_BETA1-6 : angle 1.53342 / 0.77 ( 9) link_NAG-ASN : bond 0.00579 / 0.39 ( 10) link_NAG-ASN : angle 3.94187 / 2.79 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8195 (pt) cc_final: 0.7411 (mt) REVERT: C 162 ASP cc_start: 0.8559 (p0) cc_final: 0.8260 (p0) REVERT: C 187 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7489 (mt) outliers start: 32 outliers final: 17 residues processed: 115 average time/residue: 0.0726 time to fit residues: 13.1214 Evaluate side-chains 106 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [89, 100, 65, 122, 112, 52, 69, 33, 41, 125, 23] chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088240 restraints weight = 30811.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088221 restraints weight = 36136.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.088784 restraints weight = 37421.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089742 restraints weight = 22245.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090138 restraints weight = 19456.154| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10736 Z= 0.112 Angle : 0.604 12.783 14652 Z= 0.287 Chirality : 0.046 0.559 1719 Planarity : 0.003 0.048 1874 Dihedral : 6.568 58.714 1882 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.25 % Allowed : 17.30 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.23), residues: 1362 helix: 0.76 (0.28), residues: 338 sheet: -0.93 (0.51), residues: 105 loop : -1.54 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.017 0.001 TYR D 136 PHE 0.007 0.001 PHE C 201 TRP 0.008 0.001 TRP B 218 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10700) covalent geometry : angle 0.56781 / 0.28 (14560) SS BOND : bond 0.00283 / 0.18 ( 16) SS BOND : angle 1.21862 / 0.82 ( 32) hydrogen bonds : bond 0.03285 / 2.39 ( 248) hydrogen bonds : angle 4.22019 / 2.95 ( 699) link_BETA1-4 : bond 0.00685 / 0.48 ( 7) link_BETA1-4 : angle 3.02042 / 2.34 ( 21) link_BETA1-6 : bond 0.00301 / 0.15 ( 3) link_BETA1-6 : angle 1.32415 / 0.69 ( 9) link_NAG-ASN : bond 0.00656 / 0.46 ( 10) link_NAG-ASN : angle 3.60815 / 2.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8172 (pt) cc_final: 0.7536 (mt) REVERT: C 162 ASP cc_start: 0.8534 (p0) cc_final: 0.8246 (p0) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.0789 time to fit residues: 14.1499 Evaluate side-chains 111 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [32, 118, 67, 15, 129, 12, 80, 87, 39, 116, 70] chunk 32 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 12 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.110093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088618 restraints weight = 30706.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.088727 restraints weight = 33053.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089358 restraints weight = 34508.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090088 restraints weight = 21257.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090393 restraints weight = 18845.672| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10736 Z= 0.113 Angle : 0.593 12.470 14652 Z= 0.282 Chirality : 0.046 0.542 1719 Planarity : 0.003 0.050 1874 Dihedral : 5.960 59.018 1882 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.44 % Allowed : 17.89 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.23), residues: 1362 helix: 0.84 (0.28), residues: 337 sheet: -0.91 (0.50), residues: 111 loop : -1.56 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.033 0.001 TYR B 220 PHE 0.008 0.001 PHE C 201 TRP 0.006 0.001 TRP B 368 HIS 0.001 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10700) covalent geometry : angle 0.55832 / 0.27 (14560) SS BOND : bond 0.00377 / 0.27 ( 16) SS BOND : angle 1.19281 / 0.80 ( 32) hydrogen bonds : bond 0.03083 / 2.23 ( 248) hydrogen bonds : angle 4.08845 / 2.87 ( 699) link_BETA1-4 : bond 0.00749 / 0.49 ( 7) link_BETA1-4 : angle 2.91513 / 2.16 ( 21) link_BETA1-6 : bond 0.00294 / 0.15 ( 3) link_BETA1-6 : angle 1.32625 / 0.70 ( 9) link_NAG-ASN : bond 0.00646 / 0.45 ( 10) link_NAG-ASN : angle 3.53689 / 2.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8219 (pt) cc_final: 0.7618 (mt) REVERT: C 162 ASP cc_start: 0.8579 (p0) cc_final: 0.8247 (p0) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.0688 time to fit residues: 12.7236 Evaluate side-chains 112 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 29 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [82, 30, 14, 50, 95, 127, 3, 72, 53, 34, 26] chunk 82 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089397 restraints weight = 30697.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088388 restraints weight = 33200.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089014 restraints weight = 36412.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.090801 restraints weight = 24080.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090960 restraints weight = 17293.998| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10736 Z= 0.098 Angle : 0.589 11.913 14652 Z= 0.278 Chirality : 0.045 0.496 1719 Planarity : 0.003 0.051 1874 Dihedral : 5.599 59.128 1882 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.86 % Allowed : 18.67 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.23), residues: 1362 helix: 0.77 (0.28), residues: 345 sheet: -0.79 (0.50), residues: 111 loop : -1.58 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.028 0.001 TYR B 220 PHE 0.011 0.001 PHE C 192 TRP 0.009 0.001 TRP B 368 HIS 0.002 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (10700) covalent geometry : angle 0.55718 / 0.27 (14560) SS BOND : bond 0.00288 / 0.21 ( 16) SS BOND : angle 0.92440 / 0.64 ( 32) hydrogen bonds : bond 0.02859 / 2.07 ( 248) hydrogen bonds : angle 3.96301 / 2.78 ( 699) link_BETA1-4 : bond 0.00795 / 0.50 ( 7) link_BETA1-4 : angle 2.87460 / 2.05 ( 21) link_BETA1-6 : bond 0.00341 / 0.17 ( 3) link_BETA1-6 : angle 1.26731 / 0.68 ( 9) link_NAG-ASN : bond 0.00678 / 0.47 ( 10) link_NAG-ASN : angle 3.40777 / 2.40 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8190 (pt) cc_final: 0.7655 (mt) REVERT: C 88 TYR cc_start: 0.8110 (m-80) cc_final: 0.7825 (m-80) REVERT: C 162 ASP cc_start: 0.8560 (p0) cc_final: 0.8207 (p0) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 0.0764 time to fit residues: 13.8601 Evaluate side-chains 112 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [53, 2, 91, 121, 10, 38, 83, 65, 85, 74, 134] chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.0020 chunk 91 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.109567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087538 restraints weight = 30625.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086930 restraints weight = 33928.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087750 restraints weight = 37759.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088619 restraints weight = 23078.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089021 restraints weight = 19949.166| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10736 Z= 0.128 Angle : 0.599 12.302 14652 Z= 0.286 Chirality : 0.046 0.550 1719 Planarity : 0.003 0.052 1874 Dihedral : 5.377 59.035 1882 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.05 % Allowed : 18.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.23), residues: 1362 helix: 0.78 (0.28), residues: 344 sheet: -0.92 (0.50), residues: 111 loop : -1.57 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.025 0.001 TYR B 220 PHE 0.016 0.001 PHE C 192 TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10700) covalent geometry : angle 0.56725 / 0.28 (14560) SS BOND : bond 0.00276 / 0.19 ( 16) SS BOND : angle 0.90770 / 0.65 ( 32) hydrogen bonds : bond 0.03091 / 2.26 ( 248) hydrogen bonds : angle 4.08722 / 2.89 ( 699) link_BETA1-4 : bond 0.00755 / 0.48 ( 7) link_BETA1-4 : angle 2.78304 / 1.95 ( 21) link_BETA1-6 : bond 0.00263 / 0.13 ( 3) link_BETA1-6 : angle 1.37249 / 0.71 ( 9) link_NAG-ASN : bond 0.00611 / 0.42 ( 10) link_NAG-ASN : angle 3.50860 / 2.46 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8255 (pt) cc_final: 0.7727 (mt) REVERT: C 162 ASP cc_start: 0.8548 (p0) cc_final: 0.8214 (p0) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.0746 time to fit residues: 13.0320 Evaluate side-chains 107 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 29 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [95, 51, 110, 70, 61, 127, 64, 88, 28, 67, 29] chunk 95 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 chunk 127 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.108707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086413 restraints weight = 30540.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085653 restraints weight = 33237.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.086377 restraints weight = 38552.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087396 restraints weight = 23238.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.087659 restraints weight = 20116.545| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10736 Z= 0.154 Angle : 0.626 12.110 14652 Z= 0.299 Chirality : 0.046 0.556 1719 Planarity : 0.003 0.054 1874 Dihedral : 5.445 59.103 1882 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.86 % Allowed : 18.28 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.23), residues: 1362 helix: 0.77 (0.28), residues: 343 sheet: -0.94 (0.50), residues: 112 loop : -1.59 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.025 0.001 TYR B 220 PHE 0.017 0.001 PHE C 192 TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10700) covalent geometry : angle 0.59590 / 0.29 (14560) SS BOND : bond 0.00274 / 0.19 ( 16) SS BOND : angle 0.95589 / 0.69 ( 32) hydrogen bonds : bond 0.03452 / 2.53 ( 248) hydrogen bonds : angle 4.19688 / 2.95 ( 699) link_BETA1-4 : bond 0.00756 / 0.50 ( 7) link_BETA1-4 : angle 2.70906 / 1.87 ( 21) link_BETA1-6 : bond 0.00241 / 0.12 ( 3) link_BETA1-6 : angle 1.40278 / 0.72 ( 9) link_NAG-ASN : bond 0.00590 / 0.39 ( 10) link_NAG-ASN : angle 3.52588 / 2.46 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ILE cc_start: 0.8291 (pt) cc_final: 0.7775 (mt) REVERT: C 162 ASP cc_start: 0.8621 (p0) cc_final: 0.8283 (p0) outliers start: 19 outliers final: 19 residues processed: 108 average time/residue: 0.0808 time to fit residues: 13.7196 Evaluate side-chains 109 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [97, 76, 86, 101, 43, 59, 29, 128, 114, 55, 26] chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.107092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085421 restraints weight = 31084.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085896 restraints weight = 36453.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086168 restraints weight = 39318.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087294 restraints weight = 23105.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087613 restraints weight = 19221.237| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10736 Z= 0.212 Angle : 0.686 13.729 14652 Z= 0.332 Chirality : 0.048 0.641 1719 Planarity : 0.004 0.054 1874 Dihedral : 5.764 59.293 1882 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.96 % Allowed : 18.96 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.22), residues: 1362 helix: 0.52 (0.28), residues: 344 sheet: -1.44 (0.47), residues: 121 loop : -1.68 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.025 0.002 TYR B 220 PHE 0.017 0.002 PHE C 192 TRP 0.012 0.001 TRP C 153 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (10700) covalent geometry : angle 0.65443 / 0.32 (14560) SS BOND : bond 0.00332 / 0.24 ( 16) SS BOND : angle 1.21840 / 0.87 ( 32) hydrogen bonds : bond 0.03986 / 2.91 ( 248) hydrogen bonds : angle 4.49250 / 3.15 ( 699) link_BETA1-4 : bond 0.00709 / 0.50 ( 7) link_BETA1-4 : angle 2.60285 / 1.76 ( 21) link_BETA1-6 : bond 0.00220 / 0.11 ( 3) link_BETA1-6 : angle 1.51656 / 0.75 ( 9) link_NAG-ASN : bond 0.00597 / 0.40 ( 10) link_NAG-ASN : angle 3.87173 / 2.71 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.62 seconds wall clock time: 27 minutes 34.02 seconds (1654.02 seconds total)