Starting phenix.real_space_refine on Sun Nov 17 12:33:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pzu_18045/11_2024/8pzu_18045.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 43 5.16 5 C 8660 2.51 5 N 2375 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13782 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6183 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 29, 'TRANS': 753} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2761 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 398 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1952 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 76 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.58 Number of scatterers: 13782 At special positions: 0 Unit cell: (110.11, 146.51, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 Mg 1 11.99 O 2703 8.00 N 2375 7.00 C 8660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 18 sheets defined 28.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.664A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.695A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 4.355A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.109A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.589A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.831A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.506A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 4.600A pdb=" N GLU A 689 " --> pdb=" O TYR A 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 3.947A pdb=" N GLU C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.053A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'F' and resid 39 through 53 Processing helix chain 'F' and resid 62 through 86 removed outlier: 3.538A pdb=" N ILE F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 103 Processing helix chain 'F' and resid 124 through 149 removed outlier: 3.966A pdb=" N ILE F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 Processing helix chain 'F' and resid 190 through 206 Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.988A pdb=" N ILE F 217 " --> pdb=" O GLY F 213 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 226 removed outlier: 4.334A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 239 removed outlier: 3.832A pdb=" N LEU F 239 " --> pdb=" O ILE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 249 removed outlier: 4.283A pdb=" N GLN F 245 " --> pdb=" O GLY F 241 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.763A pdb=" N MET F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.040A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 171 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.040A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 171 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.576A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER B 193 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 245 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 274 removed outlier: 4.389A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA A 343 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.072A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.961A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 454 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A 456 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 447 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE A 458 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLN A 445 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY A 460 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY A 443 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS A 462 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN A 441 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50 removed outlier: 3.753A pdb=" N THR B 45 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.100A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.188A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 5.894A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.524A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 5.900A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.204A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 32 Processing sheet with id=AB9, first strand: chain 'F' and resid 230 through 234 removed outlier: 5.510A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN F 175 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1794 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: 5.22 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4592 1.34 - 1.46: 2353 1.46 - 1.58: 7027 1.58 - 1.70: 1 1.70 - 1.82: 83 Bond restraints: 14056 Sorted by residual: bond pdb=" CA UX8 I 3 " pdb=" CB UX8 I 3 " ideal model delta sigma weight residual 1.530 1.714 -0.184 2.00e-02 2.50e+03 8.43e+01 bond pdb=" CA UX8 I 3 " pdb=" C UX8 I 3 " ideal model delta sigma weight residual 1.525 1.334 0.191 2.10e-02 2.27e+03 8.31e+01 bond pdb=" CB UX8 I 3 " pdb=" CG UX8 I 3 " ideal model delta sigma weight residual 1.493 1.648 -0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" CG UX8 I 3 " pdb=" CD2 UX8 I 3 " ideal model delta sigma weight residual 1.433 1.575 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" N UX8 I 3 " pdb=" CA UX8 I 3 " ideal model delta sigma weight residual 1.458 1.337 0.121 1.90e-02 2.77e+03 4.08e+01 ... (remaining 14051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 19062 5.24 - 10.48: 15 10.48 - 15.72: 0 15.72 - 20.97: 1 20.97 - 26.21: 1 Bond angle restraints: 19079 Sorted by residual: angle pdb=" CA UX8 I 3 " pdb=" C UX8 I 3 " pdb=" O UX8 I 3 " ideal model delta sigma weight residual 120.80 147.01 -26.21 1.70e+00 3.46e-01 2.38e+02 angle pdb=" CA UX8 I 3 " pdb=" C UX8 I 3 " pdb=" N THR I 4 " ideal model delta sigma weight residual 116.20 95.86 20.34 2.00e+00 2.50e-01 1.03e+02 angle pdb=" O UX8 I 3 " pdb=" C UX8 I 3 " pdb=" N THR I 4 " ideal model delta sigma weight residual 123.00 117.13 5.87 1.60e+00 3.91e-01 1.35e+01 angle pdb=" C UX8 I 3 " pdb=" N THR I 4 " pdb=" CA THR I 4 " ideal model delta sigma weight residual 121.70 128.19 -6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CD1 UX8 I 3 " pdb=" NE1 UX8 I 3 " pdb=" CE2 UX8 I 3 " ideal model delta sigma weight residual 109.40 119.72 -10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 19074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 7618 18.19 - 36.39: 627 36.39 - 54.58: 82 54.58 - 72.78: 23 72.78 - 90.97: 13 Dihedral angle restraints: 8363 sinusoidal: 3289 harmonic: 5074 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 133.35 -40.35 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA GLU A 521 " pdb=" C GLU A 521 " pdb=" N TYR A 522 " pdb=" CA TYR A 522 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA THR A 288 " pdb=" C THR A 288 " pdb=" N LYS A 289 " pdb=" CA LYS A 289 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 8360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1957 0.092 - 0.185: 136 0.185 - 0.277: 2 0.277 - 0.370: 1 0.370 - 0.462: 1 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CB UX8 I 3 " pdb=" CA UX8 I 3 " pdb=" CG UX8 I 3 " pdb=" O9 UX8 I 3 " both_signs ideal model delta sigma weight residual False -2.38 -2.84 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA UX8 I 3 " pdb=" N UX8 I 3 " pdb=" C UX8 I 3 " pdb=" CB UX8 I 3 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB THR B 386 " pdb=" CA THR B 386 " pdb=" OG1 THR B 386 " pdb=" CG2 THR B 386 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2094 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 46 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 47 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 47 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 47 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 778 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 779 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 779 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 779 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 239 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO F 240 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 240 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 240 " 0.022 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 166 2.59 - 3.16: 11854 3.16 - 3.74: 22625 3.74 - 4.32: 31581 4.32 - 4.90: 51811 Nonbonded interactions: 118037 Sorted by model distance: nonbonded pdb=" OD1 ASP B 212 " pdb="MG MG B 401 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP B 248 " pdb="MG MG B 401 " model vdw 2.060 2.170 nonbonded pdb=" O GLY B 196 " pdb="MG MG B 401 " model vdw 2.065 2.170 nonbonded pdb=" OG SER B 126 " pdb=" O GLN B 130 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.197 3.040 ... (remaining 118032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.670 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.005 0.191 14056 Z= 0.304 Angle : 0.640 26.208 19079 Z= 0.344 Chirality : 0.045 0.462 2097 Planarity : 0.004 0.050 2514 Dihedral : 13.738 90.973 5120 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1737 helix: 1.42 (0.24), residues: 451 sheet: -0.80 (0.23), residues: 473 loop : -0.78 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.003 0.001 HIS A 555 PHE 0.024 0.001 PHE A 140 TYR 0.013 0.001 TYR A 522 ARG 0.010 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.465 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 413 ASP cc_start: 0.7769 (m-30) cc_final: 0.7551 (m-30) REVERT: D 128 PHE cc_start: 0.3921 (t80) cc_final: 0.3674 (m-10) REVERT: D 201 MET cc_start: 0.8037 (mmm) cc_final: 0.7575 (mtt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2785 time to fit residues: 72.1527 Evaluate side-chains 137 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14056 Z= 0.192 Angle : 0.552 6.951 19079 Z= 0.294 Chirality : 0.044 0.184 2097 Planarity : 0.004 0.058 2514 Dihedral : 4.361 18.085 1922 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.68 % Allowed : 6.77 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1737 helix: 1.49 (0.24), residues: 455 sheet: -0.77 (0.24), residues: 443 loop : -0.72 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS F 178 PHE 0.015 0.001 PHE A 140 TYR 0.015 0.001 TYR D 62 ARG 0.005 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.494 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: D 109 MET cc_start: 0.7372 (mtp) cc_final: 0.7170 (mtp) REVERT: D 128 PHE cc_start: 0.3770 (t80) cc_final: 0.3508 (m-10) REVERT: F 186 ASN cc_start: 0.7577 (m-40) cc_final: 0.7367 (m-40) outliers start: 10 outliers final: 8 residues processed: 163 average time/residue: 0.2827 time to fit residues: 68.1173 Evaluate side-chains 149 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 158 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN F 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14056 Z= 0.375 Angle : 0.631 9.041 19079 Z= 0.335 Chirality : 0.046 0.193 2097 Planarity : 0.005 0.060 2514 Dihedral : 4.798 17.371 1922 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.42 % Allowed : 9.75 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1737 helix: 1.24 (0.23), residues: 451 sheet: -1.03 (0.23), residues: 459 loop : -0.84 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 233 HIS 0.004 0.001 HIS D 102 PHE 0.014 0.002 PHE I 7 TYR 0.016 0.002 TYR A 618 ARG 0.005 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.632 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: D 128 PHE cc_start: 0.3805 (t80) cc_final: 0.3483 (m-10) REVERT: F 413 TRP cc_start: 0.8408 (t60) cc_final: 0.8134 (t60) outliers start: 21 outliers final: 18 residues processed: 159 average time/residue: 0.2766 time to fit residues: 65.6060 Evaluate side-chains 153 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 555 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14056 Z= 0.180 Angle : 0.539 7.949 19079 Z= 0.285 Chirality : 0.043 0.178 2097 Planarity : 0.004 0.060 2514 Dihedral : 4.485 18.758 1922 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 1.42 % Allowed : 11.78 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1737 helix: 1.47 (0.24), residues: 451 sheet: -0.97 (0.23), residues: 454 loop : -0.75 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.003 0.001 HIS F 178 PHE 0.015 0.001 PHE A 426 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.449 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 739 TRP cc_start: 0.7800 (t60) cc_final: 0.7460 (t60) REVERT: D 128 PHE cc_start: 0.3756 (t80) cc_final: 0.3403 (m-10) REVERT: F 413 TRP cc_start: 0.8286 (t60) cc_final: 0.7952 (t60) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.2634 time to fit residues: 65.4964 Evaluate side-chains 152 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN E 34 GLN E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14056 Z= 0.196 Angle : 0.536 7.350 19079 Z= 0.283 Chirality : 0.043 0.177 2097 Planarity : 0.004 0.060 2514 Dihedral : 4.423 18.264 1922 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 1.69 % Allowed : 12.39 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1737 helix: 1.55 (0.24), residues: 452 sheet: -0.92 (0.23), residues: 459 loop : -0.73 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS F 178 PHE 0.014 0.001 PHE A 426 TYR 0.015 0.001 TYR B 388 ARG 0.011 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.757 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 289 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7741 (mmmt) REVERT: A 739 TRP cc_start: 0.7804 (t60) cc_final: 0.7478 (t60) REVERT: D 128 PHE cc_start: 0.3796 (t80) cc_final: 0.3388 (m-10) REVERT: F 413 TRP cc_start: 0.8323 (t60) cc_final: 0.8021 (t60) outliers start: 25 outliers final: 21 residues processed: 171 average time/residue: 0.2694 time to fit residues: 68.2570 Evaluate side-chains 162 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 58 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN F 33 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14056 Z= 0.214 Angle : 0.537 7.309 19079 Z= 0.285 Chirality : 0.043 0.185 2097 Planarity : 0.004 0.059 2514 Dihedral : 4.433 17.698 1922 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 2.30 % Allowed : 12.32 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1737 helix: 1.52 (0.24), residues: 452 sheet: -0.91 (0.23), residues: 467 loop : -0.75 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS F 178 PHE 0.014 0.001 PHE A 426 TYR 0.016 0.001 TYR B 388 ARG 0.008 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.683 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 739 TRP cc_start: 0.7786 (t60) cc_final: 0.7479 (t60) REVERT: B 221 MET cc_start: 0.8701 (tpt) cc_final: 0.8374 (tpt) REVERT: D 128 PHE cc_start: 0.3757 (t80) cc_final: 0.3367 (m-10) REVERT: F 413 TRP cc_start: 0.8369 (t60) cc_final: 0.8032 (t60) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.2902 time to fit residues: 78.9767 Evaluate side-chains 163 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 414 MET Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 166 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 286 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14056 Z= 0.213 Angle : 0.543 7.663 19079 Z= 0.287 Chirality : 0.043 0.178 2097 Planarity : 0.004 0.058 2514 Dihedral : 4.427 17.649 1922 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.12 % Favored : 94.82 % Rotamer: Outliers : 1.90 % Allowed : 12.73 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1737 helix: 1.53 (0.24), residues: 452 sheet: -0.89 (0.23), residues: 471 loop : -0.75 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS F 178 PHE 0.014 0.001 PHE A 426 TYR 0.015 0.001 TYR B 388 ARG 0.013 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.507 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: D 128 PHE cc_start: 0.3739 (t80) cc_final: 0.3364 (m-10) REVERT: F 413 TRP cc_start: 0.8361 (t60) cc_final: 0.8058 (t60) outliers start: 28 outliers final: 26 residues processed: 168 average time/residue: 0.2648 time to fit residues: 65.7741 Evaluate side-chains 167 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 414 MET Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14056 Z= 0.293 Angle : 0.581 7.594 19079 Z= 0.308 Chirality : 0.044 0.180 2097 Planarity : 0.004 0.058 2514 Dihedral : 4.623 18.114 1922 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 2.44 % Allowed : 12.73 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1737 helix: 1.34 (0.24), residues: 457 sheet: -1.01 (0.23), residues: 472 loop : -0.80 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 183 HIS 0.003 0.001 HIS A 677 PHE 0.013 0.002 PHE A 140 TYR 0.016 0.002 TYR B 388 ARG 0.008 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.627 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: D 128 PHE cc_start: 0.3790 (t80) cc_final: 0.3407 (m-10) REVERT: F 413 TRP cc_start: 0.8451 (t60) cc_final: 0.8146 (t60) outliers start: 36 outliers final: 30 residues processed: 171 average time/residue: 0.2639 time to fit residues: 67.2295 Evaluate side-chains 165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 414 MET Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.0970 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14056 Z= 0.242 Angle : 0.574 9.397 19079 Z= 0.303 Chirality : 0.044 0.217 2097 Planarity : 0.004 0.058 2514 Dihedral : 4.574 19.683 1922 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 2.10 % Allowed : 13.74 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1737 helix: 1.37 (0.24), residues: 460 sheet: -1.01 (0.23), residues: 473 loop : -0.79 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 739 HIS 0.002 0.001 HIS A 196 PHE 0.013 0.001 PHE A 426 TYR 0.013 0.001 TYR D 184 ARG 0.016 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.580 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 87 GLN cc_start: 0.4441 (tm-30) cc_final: 0.2980 (mt0) REVERT: D 128 PHE cc_start: 0.3766 (t80) cc_final: 0.3379 (m-10) REVERT: E 29 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7245 (ptp90) REVERT: F 413 TRP cc_start: 0.8430 (t60) cc_final: 0.8127 (t60) outliers start: 31 outliers final: 31 residues processed: 165 average time/residue: 0.2634 time to fit residues: 65.1642 Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 414 MET Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 158 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14056 Z= 0.410 Angle : 0.660 8.342 19079 Z= 0.350 Chirality : 0.047 0.237 2097 Planarity : 0.005 0.059 2514 Dihedral : 4.978 21.215 1922 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 2.37 % Allowed : 13.61 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1737 helix: 1.08 (0.24), residues: 457 sheet: -1.09 (0.23), residues: 469 loop : -1.00 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 739 HIS 0.004 0.001 HIS B 121 PHE 0.015 0.002 PHE A 140 TYR 0.017 0.002 TYR A 608 ARG 0.011 0.001 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.577 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 87 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. REVERT: A 90 GLU cc_start: 0.5295 (mp0) cc_final: 0.5047 (mp0) REVERT: D 219 GLU cc_start: 0.7285 (tt0) cc_final: 0.7003 (tt0) REVERT: E 29 ARG cc_start: 0.7774 (ptp-110) cc_final: 0.7357 (ptp90) REVERT: F 413 TRP cc_start: 0.8521 (t60) cc_final: 0.8191 (t60) outliers start: 35 outliers final: 30 residues processed: 172 average time/residue: 0.2662 time to fit residues: 67.4198 Evaluate side-chains 171 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 414 MET Chi-restraints excluded: chain I residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 59 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 = 0.3764 r_free = 0.3764 target = 0.116300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094405 restraints weight = 27951.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094422 restraints weight = 17805.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094891 restraints weight = 16279.247| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14056 Z= 0.205 Angle : 0.573 9.413 19079 Z= 0.303 Chirality : 0.044 0.193 2097 Planarity : 0.004 0.059 2514 Dihedral : 4.639 20.278 1922 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 1.69 % Allowed : 14.62 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1737 helix: 1.24 (0.24), residues: 454 sheet: -1.04 (0.23), residues: 481 loop : -0.82 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 739 HIS 0.002 0.001 HIS F 178 PHE 0.016 0.001 PHE A 140 TYR 0.015 0.001 TYR D 62 ARG 0.010 0.000 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.94 seconds wall clock time: 48 minutes 55.72 seconds (2935.72 seconds total)