Starting phenix.real_space_refine on Sun Apr 5 20:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t3y_55521/04_2026/9t3y_55521.map" } resolution = 3.44 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= 0.001 sd= 0.024 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 2 7.51 5 S 69 5.16 5 C 8097 2.51 5 N 2237 2.21 5 O 2527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12937 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5803 Classifications: {'peptide': 751} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 715} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3573 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain: "C" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3286 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 1 Chain: "D" 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: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 3, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.19 Number of scatterers: 12937 At special positions: 0 Unit cell: (97.05, 155.28, 214.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 Ca 5 19.99 S 69 16.00 O 2527 8.00 N 2237 7.00 C 8097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.04 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 409 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 241 " distance=2.02 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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-ASN " NAG A1205 " - " ASN A 677 " " NAG A1206 " - " ASN A 681 " " NAG B2004 " - " ASN B 232 " " NAG D 1 " - " ASN A 719 " " NAG E 1 " - " ASN A 70 " " NAG F 1 " - " ASN A 375 " " NAG G 1 " - " ASN B 190 " " NAG H 1 " - " ASN B 94 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 476.4 milliseconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 19 sheets defined 27.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 146 through 164 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.614A pdb=" N LYS A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.748A pdb=" N GLY A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.810A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.407A pdb=" N PHE A 275 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.856A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.646A pdb=" N SER A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 562' Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.849A pdb=" N GLY B 18 " --> pdb=" O CYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.690A pdb=" N GLY B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.764A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.545A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.529A pdb=" N SER B 274 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 275 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 277 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 304 through 313 removed outlier: 3.627A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 3.654A pdb=" N VAL B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.667A pdb=" N GLY B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.589A pdb=" N ILE B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.694A pdb=" N LYS C 84 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.356A pdb=" N PHE C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 removed outlier: 3.725A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 removed outlier: 3.543A pdb=" N ALA C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.796A pdb=" N LEU C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.577A pdb=" N LEU C 216 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 237 Processing helix chain 'C' and resid 247 through 263 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 308 through 326 removed outlier: 3.648A pdb=" N LEU C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.671A pdb=" N VAL C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 368 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.601A pdb=" N THR C 404 " --> pdb=" O PRO C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.699A pdb=" N MET A 9 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 585 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 575 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.657A pdb=" N GLN A 36 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG A 44 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 4.210A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184 removed outlier: 5.520A pdb=" N ILE A 182 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 175 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 184 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP A 134 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 238 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A 136 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 240 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 138 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS A 235 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR A 267 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 237 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 269 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 239 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 397 removed outlier: 3.971A pdb=" N ALA A 391 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 430 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG A 420 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER A 428 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN A 422 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TRP A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.507A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 492 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.507A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY A 472 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 509 through 513 removed outlier: 5.869A pdb=" N ASP A 522 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 removed outlier: 4.058A pdb=" N GLY A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 630 through 631 removed outlier: 3.703A pdb=" N LYS A 631 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 703 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 630 through 631 removed outlier: 3.703A pdb=" N LYS A 631 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 703 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 683 through 690 Processing sheet with id=AB5, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.723A pdb=" N LEU B 85 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 76 through 77 removed outlier: 6.973A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 183 through 189 removed outlier: 5.217A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 188 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 105 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLY B 145 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 107 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY B 147 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR B 109 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE B 149 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET B 111 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG B 235 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 297 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 237 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 299 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 239 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 8 Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.672A pdb=" N ALA C 34 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG C 39 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3494 1.33 - 1.45: 2745 1.45 - 1.58: 6836 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 13172 Sorted by residual: bond pdb=" C GLU C 412 " pdb=" O GLU C 412 " ideal model delta sigma weight residual 1.234 1.301 -0.068 1.24e-02 6.50e+03 2.98e+01 bond pdb=" C GLU C 412 " pdb=" N TRP C 413 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.41e-02 5.03e+03 1.05e+01 bond pdb=" N ILE B 38 " pdb=" CA ILE B 38 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.24e-02 6.50e+03 9.60e+00 bond pdb=" N VAL C 336 " pdb=" CA VAL C 336 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.54e+00 bond pdb=" N ASP B 34 " pdb=" CA ASP B 34 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.16e-02 7.43e+03 9.50e+00 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 17541 3.81 - 7.61: 240 7.61 - 11.42: 35 11.42 - 15.22: 11 15.22 - 19.03: 4 Bond angle restraints: 17831 Sorted by residual: angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 128.43 -14.33 2.00e+00 2.50e-01 5.14e+01 angle pdb=" N TYR C 33 " pdb=" CA TYR C 33 " pdb=" C TYR C 33 " ideal model delta sigma weight residual 109.40 120.87 -11.47 1.63e+00 3.76e-01 4.95e+01 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 131.73 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" N MET A 153 " pdb=" CA MET A 153 " pdb=" CB MET A 153 " ideal model delta sigma weight residual 110.40 120.42 -10.02 1.63e+00 3.76e-01 3.78e+01 angle pdb=" CA ARG B 43 " pdb=" CB ARG B 43 " pdb=" CG ARG B 43 " ideal model delta sigma weight residual 114.10 126.35 -12.25 2.00e+00 2.50e-01 3.75e+01 ... (remaining 17826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 7503 24.65 - 49.30: 591 49.30 - 73.95: 91 73.95 - 98.60: 29 98.60 - 123.26: 18 Dihedral angle restraints: 8232 sinusoidal: 3573 harmonic: 4659 Sorted by residual: dihedral pdb=" CA SER A 82 " pdb=" C SER A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual -180.00 -115.54 -64.46 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 176 " pdb=" CB CYS B 176 " ideal model delta sinusoidal sigma weight residual 93.00 163.81 -70.81 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 150.52 -57.52 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 8229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1950 0.141 - 0.282: 67 0.282 - 0.424: 3 0.424 - 0.565: 4 0.565 - 0.706: 2 Chirality restraints: 2026 Sorted by residual: chirality pdb=" CG LEU C 294 " pdb=" CB LEU C 294 " pdb=" CD1 LEU C 294 " pdb=" CD2 LEU C 294 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG A1205 " pdb=" ND2 ASN A 677 " pdb=" C2 NAG A1205 " pdb=" O5 NAG A1205 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA TYR C 33 " pdb=" N TYR C 33 " pdb=" C TYR C 33 " pdb=" CB TYR C 33 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.84e+00 ... (remaining 2023 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 300 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LYS C 300 " -0.079 2.00e-02 2.50e+03 pdb=" O LYS C 300 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN C 301 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 33 " 0.015 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR C 33 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR C 33 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C 33 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 33 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 33 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 33 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 313 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG A 313 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 313 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 313 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 313 " -0.010 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 54 2.56 - 3.15: 9648 3.15 - 3.73: 20575 3.73 - 4.31: 28057 4.31 - 4.90: 46273 Nonbonded interactions: 104607 Sorted by model distance: nonbonded pdb=" OD1 ASP C 330 " pdb="MN MN A1203 " model vdw 1.975 2.320 nonbonded pdb="MN MN A1203 " pdb=" O HOH A1303 " model vdw 2.062 2.320 nonbonded pdb="MN MN A1203 " pdb=" O HOH C 501 " model vdw 2.064 2.320 nonbonded pdb=" OE1 GLU A 320 " pdb="MN MN B2001 " model vdw 2.065 2.320 nonbonded pdb=" OG SER A 142 " pdb="MN MN A1203 " model vdw 2.068 2.320 ... (remaining 104602 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 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.980 Find NCS groups from input model: 0.080 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.008 0.068 13212 Z= 0.391 Angle : 1.236 19.030 17931 Z= 0.652 Chirality : 0.070 0.706 2026 Planarity : 0.009 0.131 2325 Dihedral : 18.725 123.256 5190 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.54 % Favored : 94.21 % Rotamer: Outliers : 1.45 % Allowed : 21.01 % Favored : 77.54 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.18), residues: 1624 helix: -2.19 (0.21), residues: 363 sheet: -0.76 (0.23), residues: 436 loop : -2.01 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 418 TYR 0.063 0.003 TYR C 33 PHE 0.042 0.003 PHE C 416 TRP 0.027 0.002 TRP C 413 HIS 0.013 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00767 (13172) covalent geometry : angle 1.21400 (17831) SS BOND : bond 0.00304 ( 20) SS BOND : angle 1.39964 ( 40) hydrogen bonds : bond 0.14743 ( 473) hydrogen bonds : angle 7.52358 ( 1305) link_ALPHA1-3 : bond 0.01117 ( 2) link_ALPHA1-3 : angle 2.54522 ( 6) link_ALPHA1-6 : bond 0.00091 ( 2) link_ALPHA1-6 : angle 1.45740 ( 6) link_BETA1-4 : bond 0.00777 ( 8) link_BETA1-4 : angle 3.63223 ( 24) link_NAG-ASN : bond 0.01603 ( 8) link_NAG-ASN : angle 5.24407 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8919 (mmm) cc_final: 0.8660 (mmm) REVERT: A 580 MET cc_start: 0.8937 (mtm) cc_final: 0.8391 (tmm) REVERT: B 57 MET cc_start: 0.3983 (mpp) cc_final: 0.3160 (mtm) REVERT: B 208 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8780 (tt) REVERT: B 247 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8775 (p90) REVERT: B 279 TYR cc_start: 0.9278 (m-80) cc_final: 0.8906 (m-80) REVERT: C 33 TYR cc_start: 0.1628 (OUTLIER) cc_final: 0.1115 (m-80) REVERT: C 98 MET cc_start: 0.0330 (mtt) cc_final: 0.0038 (mtm) REVERT: C 212 MET cc_start: -0.1501 (mtt) cc_final: -0.2332 (ttt) REVERT: C 282 MET cc_start: 0.5815 (pmm) cc_final: 0.4958 (ptp) outliers start: 20 outliers final: 9 residues processed: 75 average time/residue: 0.0962 time to fit residues: 11.3903 Evaluate side-chains 61 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.0170 chunk 149 optimal weight: 40.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 24 GLN A 36 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.120252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077533 restraints weight = 49763.199| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.98 r_work: 0.3196 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13212 Z= 0.119 Angle : 0.659 10.159 17931 Z= 0.320 Chirality : 0.046 0.391 2026 Planarity : 0.005 0.062 2325 Dihedral : 10.818 110.209 2195 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.69 % Favored : 96.06 % Rotamer: Outliers : 2.83 % Allowed : 19.64 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.63 (0.20), residues: 1624 helix: -0.54 (0.25), residues: 359 sheet: -0.59 (0.24), residues: 419 loop : -1.57 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 647 TYR 0.013 0.001 TYR B 308 PHE 0.020 0.001 PHE A 121 TRP 0.010 0.001 TRP C 413 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00250 (13172) covalent geometry : angle 0.63098 (17831) SS BOND : bond 0.00174 ( 20) SS BOND : angle 0.83068 ( 40) hydrogen bonds : bond 0.03365 ( 473) hydrogen bonds : angle 5.59041 ( 1305) link_ALPHA1-3 : bond 0.00901 ( 2) link_ALPHA1-3 : angle 2.81459 ( 6) link_ALPHA1-6 : bond 0.00360 ( 2) link_ALPHA1-6 : angle 2.32184 ( 6) link_BETA1-4 : bond 0.00402 ( 8) link_BETA1-4 : angle 2.93243 ( 24) link_NAG-ASN : bond 0.00797 ( 8) link_NAG-ASN : angle 3.99403 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 49 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8818 (p0) REVERT: A 580 MET cc_start: 0.8889 (mtm) cc_final: 0.8653 (tmm) REVERT: A 717 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8078 (ptm-80) REVERT: B 57 MET cc_start: 0.3773 (mpp) cc_final: 0.3162 (mtm) REVERT: B 125 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9039 (mttm) REVERT: B 279 TYR cc_start: 0.9180 (m-80) cc_final: 0.8808 (m-80) REVERT: B 304 MET cc_start: 0.7940 (mmm) cc_final: 0.7707 (mmm) REVERT: C 33 TYR cc_start: 0.1007 (OUTLIER) cc_final: 0.0807 (m-80) REVERT: C 98 MET cc_start: -0.2194 (mtt) cc_final: -0.2429 (mtp) outliers start: 39 outliers final: 16 residues processed: 84 average time/residue: 0.1081 time to fit residues: 13.7916 Evaluate side-chains 65 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 133 optimal weight: 40.0000 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.119054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075032 restraints weight = 49506.646| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.18 r_work: 0.3133 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13212 Z= 0.210 Angle : 0.663 10.916 17931 Z= 0.326 Chirality : 0.046 0.357 2026 Planarity : 0.004 0.060 2325 Dihedral : 8.728 108.483 2188 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.50 % Rotamer: Outliers : 3.62 % Allowed : 18.99 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.27 (0.20), residues: 1624 helix: 0.27 (0.27), residues: 360 sheet: -0.66 (0.23), residues: 439 loop : -1.42 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 302 TYR 0.017 0.001 TYR A 390 PHE 0.023 0.001 PHE A 121 TRP 0.017 0.001 TRP C 413 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00465 (13172) covalent geometry : angle 0.63512 (17831) SS BOND : bond 0.00151 ( 20) SS BOND : angle 0.71488 ( 40) hydrogen bonds : bond 0.03242 ( 473) hydrogen bonds : angle 5.27492 ( 1305) link_ALPHA1-3 : bond 0.00892 ( 2) link_ALPHA1-3 : angle 2.58026 ( 6) link_ALPHA1-6 : bond 0.00372 ( 2) link_ALPHA1-6 : angle 2.69880 ( 6) link_BETA1-4 : bond 0.00428 ( 8) link_BETA1-4 : angle 2.85397 ( 24) link_NAG-ASN : bond 0.00970 ( 8) link_NAG-ASN : angle 3.99199 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 45 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7511 (mpp) cc_final: 0.7070 (mpp) REVERT: A 173 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6826 (tp) REVERT: A 174 MET cc_start: 0.5373 (tpp) cc_final: 0.5024 (tpp) REVERT: A 431 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8912 (p0) REVERT: A 717 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8132 (ptm-80) REVERT: B 57 MET cc_start: 0.3913 (mpp) cc_final: 0.3205 (mtm) REVERT: B 279 TYR cc_start: 0.9207 (m-80) cc_final: 0.8800 (m-80) REVERT: C 421 MET cc_start: 0.3175 (ppp) cc_final: 0.2909 (ppp) outliers start: 50 outliers final: 28 residues processed: 90 average time/residue: 0.1002 time to fit residues: 14.0545 Evaluate side-chains 75 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 85 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS A 431 ASN B 45 GLN B 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.118661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069957 restraints weight = 48882.549| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.97 r_work: 0.3029 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 13212 Z= 0.400 Angle : 0.818 10.257 17931 Z= 0.404 Chirality : 0.050 0.367 2026 Planarity : 0.005 0.068 2325 Dihedral : 8.844 117.040 2186 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.30 % Favored : 94.46 % Rotamer: Outliers : 3.91 % Allowed : 19.49 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.33 (0.20), residues: 1624 helix: 0.44 (0.27), residues: 363 sheet: -0.73 (0.23), residues: 443 loop : -1.57 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 43 TYR 0.027 0.002 TYR A 390 PHE 0.033 0.002 PHE A 121 TRP 0.018 0.002 TRP C 413 HIS 0.011 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00896 (13172) covalent geometry : angle 0.79287 (17831) SS BOND : bond 0.00342 ( 20) SS BOND : angle 1.19929 ( 40) hydrogen bonds : bond 0.03728 ( 473) hydrogen bonds : angle 5.45583 ( 1305) link_ALPHA1-3 : bond 0.00660 ( 2) link_ALPHA1-3 : angle 2.92328 ( 6) link_ALPHA1-6 : bond 0.00218 ( 2) link_ALPHA1-6 : angle 3.06813 ( 6) link_BETA1-4 : bond 0.00642 ( 8) link_BETA1-4 : angle 2.99293 ( 24) link_NAG-ASN : bond 0.01152 ( 8) link_NAG-ASN : angle 4.11451 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 44 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6593 (mm) REVERT: A 153 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7537 (mpp) REVERT: A 173 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7254 (tp) REVERT: A 174 MET cc_start: 0.5409 (tpp) cc_final: 0.5053 (tpp) REVERT: A 337 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: A 431 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.9003 (p0) REVERT: A 717 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8268 (ptm-80) REVERT: B 57 MET cc_start: 0.4574 (mpp) cc_final: 0.3676 (mtm) REVERT: B 115 TYR cc_start: 0.9154 (t80) cc_final: 0.8879 (t80) REVERT: B 247 PHE cc_start: 0.9557 (OUTLIER) cc_final: 0.7977 (p90) outliers start: 54 outliers final: 34 residues processed: 91 average time/residue: 0.0948 time to fit residues: 13.7570 Evaluate side-chains 83 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 42 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 502 TRP Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 30 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 110 optimal weight: 0.0980 chunk 113 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN A 431 ASN B 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.119204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.074500 restraints weight = 48840.493| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.91 r_work: 0.3128 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13212 Z= 0.120 Angle : 0.637 10.415 17931 Z= 0.309 Chirality : 0.046 0.346 2026 Planarity : 0.004 0.059 2325 Dihedral : 8.274 112.928 2186 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.31 % Favored : 95.57 % Rotamer: Outliers : 3.48 % Allowed : 20.07 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1624 helix: 0.82 (0.28), residues: 360 sheet: -0.52 (0.23), residues: 453 loop : -1.47 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.013 0.001 TYR B 308 PHE 0.033 0.001 PHE A 121 TRP 0.017 0.001 TRP C 413 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00259 (13172) covalent geometry : angle 0.61167 (17831) SS BOND : bond 0.00198 ( 20) SS BOND : angle 0.71227 ( 40) hydrogen bonds : bond 0.02949 ( 473) hydrogen bonds : angle 5.09313 ( 1305) link_ALPHA1-3 : bond 0.00970 ( 2) link_ALPHA1-3 : angle 2.78152 ( 6) link_ALPHA1-6 : bond 0.00860 ( 2) link_ALPHA1-6 : angle 2.48444 ( 6) link_BETA1-4 : bond 0.00378 ( 8) link_BETA1-4 : angle 2.81260 ( 24) link_NAG-ASN : bond 0.00775 ( 8) link_NAG-ASN : angle 3.54178 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 46 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7337 (mpp) REVERT: A 174 MET cc_start: 0.5401 (tpp) cc_final: 0.5105 (tpp) REVERT: A 376 MET cc_start: 0.8949 (mmm) cc_final: 0.8707 (mmm) REVERT: A 717 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8288 (ptm-80) REVERT: B 57 MET cc_start: 0.4479 (mpp) cc_final: 0.3503 (mtm) REVERT: B 115 TYR cc_start: 0.9011 (t80) cc_final: 0.8759 (t80) REVERT: B 279 TYR cc_start: 0.9129 (m-80) cc_final: 0.8802 (m-80) REVERT: C 248 LEU cc_start: -0.1603 (OUTLIER) cc_final: -0.2015 (mt) REVERT: C 421 MET cc_start: 0.2049 (ppp) cc_final: 0.1190 (ppp) outliers start: 48 outliers final: 30 residues processed: 87 average time/residue: 0.0923 time to fit residues: 12.8363 Evaluate side-chains 75 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 42 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 40.0000 chunk 144 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 106 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 163 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.077184 restraints weight = 49301.706| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 6.32 r_work: 0.3037 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13212 Z= 0.177 Angle : 0.646 10.982 17931 Z= 0.313 Chirality : 0.046 0.347 2026 Planarity : 0.004 0.058 2325 Dihedral : 8.068 112.796 2186 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 3.62 % Allowed : 20.22 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.21), residues: 1624 helix: 0.98 (0.28), residues: 360 sheet: -0.53 (0.23), residues: 451 loop : -1.37 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 302 TYR 0.014 0.001 TYR A 390 PHE 0.027 0.001 PHE A 121 TRP 0.019 0.001 TRP C 413 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00392 (13172) covalent geometry : angle 0.62200 (17831) SS BOND : bond 0.00208 ( 20) SS BOND : angle 0.67825 ( 40) hydrogen bonds : bond 0.02944 ( 473) hydrogen bonds : angle 5.05084 ( 1305) link_ALPHA1-3 : bond 0.00883 ( 2) link_ALPHA1-3 : angle 2.67992 ( 6) link_ALPHA1-6 : bond 0.00678 ( 2) link_ALPHA1-6 : angle 2.71422 ( 6) link_BETA1-4 : bond 0.00399 ( 8) link_BETA1-4 : angle 2.79053 ( 24) link_NAG-ASN : bond 0.00791 ( 8) link_NAG-ASN : angle 3.49759 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 43 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7395 (mpp) REVERT: A 357 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8991 (m-30) REVERT: A 376 MET cc_start: 0.8997 (mmm) cc_final: 0.8663 (mmm) REVERT: A 717 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8216 (ptm-80) REVERT: B 57 MET cc_start: 0.4197 (mpp) cc_final: 0.3363 (mtm) REVERT: B 279 TYR cc_start: 0.9194 (m-80) cc_final: 0.8854 (m-80) REVERT: C 85 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7359 (p-80) REVERT: C 98 MET cc_start: -0.4395 (ptp) cc_final: -0.4628 (ptp) REVERT: C 102 THR cc_start: 0.1877 (OUTLIER) cc_final: 0.1583 (p) REVERT: C 248 LEU cc_start: -0.0860 (OUTLIER) cc_final: -0.1463 (mt) REVERT: C 421 MET cc_start: 0.2361 (ppp) cc_final: 0.2097 (ppp) outliers start: 50 outliers final: 30 residues processed: 86 average time/residue: 0.0813 time to fit residues: 11.3908 Evaluate side-chains 78 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 42 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 127 optimal weight: 0.0370 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.074809 restraints weight = 48513.471| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.22 r_work: 0.3102 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13212 Z= 0.132 Angle : 0.632 12.623 17931 Z= 0.305 Chirality : 0.046 0.345 2026 Planarity : 0.004 0.055 2325 Dihedral : 7.815 111.869 2186 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.90 % Allowed : 20.94 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1624 helix: 1.03 (0.28), residues: 360 sheet: -0.41 (0.23), residues: 435 loop : -1.32 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.012 0.001 TYR B 308 PHE 0.027 0.001 PHE A 121 TRP 0.019 0.001 TRP C 413 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00290 (13172) covalent geometry : angle 0.60912 (17831) SS BOND : bond 0.00170 ( 20) SS BOND : angle 0.61263 ( 40) hydrogen bonds : bond 0.02808 ( 473) hydrogen bonds : angle 4.94746 ( 1305) link_ALPHA1-3 : bond 0.01018 ( 2) link_ALPHA1-3 : angle 2.66549 ( 6) link_ALPHA1-6 : bond 0.00964 ( 2) link_ALPHA1-6 : angle 2.51303 ( 6) link_BETA1-4 : bond 0.00409 ( 8) link_BETA1-4 : angle 2.75726 ( 24) link_NAG-ASN : bond 0.00738 ( 8) link_NAG-ASN : angle 3.34120 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 43 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7357 (mpp) REVERT: A 312 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 376 MET cc_start: 0.8996 (mmm) cc_final: 0.8667 (mmm) REVERT: A 717 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8205 (ptm-80) REVERT: B 57 MET cc_start: 0.3932 (mpp) cc_final: 0.3062 (mtm) REVERT: B 279 TYR cc_start: 0.9142 (m-80) cc_final: 0.8842 (m-80) REVERT: C 85 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7307 (p-80) REVERT: C 248 LEU cc_start: -0.0781 (OUTLIER) cc_final: -0.1423 (mt) outliers start: 40 outliers final: 32 residues processed: 77 average time/residue: 0.1007 time to fit residues: 12.3538 Evaluate side-chains 79 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 42 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 148 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 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 = 0.4491 r_free = 0.4491 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075491 restraints weight = 48327.926| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.96 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13212 Z= 0.114 Angle : 0.623 14.302 17931 Z= 0.299 Chirality : 0.046 0.346 2026 Planarity : 0.004 0.054 2325 Dihedral : 7.517 110.430 2186 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.04 % Allowed : 20.94 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1624 helix: 1.11 (0.28), residues: 360 sheet: -0.36 (0.24), residues: 434 loop : -1.24 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.012 0.001 TYR B 308 PHE 0.023 0.001 PHE A 121 TRP 0.020 0.001 TRP C 413 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00250 (13172) covalent geometry : angle 0.60152 (17831) SS BOND : bond 0.00165 ( 20) SS BOND : angle 0.61816 ( 40) hydrogen bonds : bond 0.02696 ( 473) hydrogen bonds : angle 4.87575 ( 1305) link_ALPHA1-3 : bond 0.00978 ( 2) link_ALPHA1-3 : angle 2.51814 ( 6) link_ALPHA1-6 : bond 0.01203 ( 2) link_ALPHA1-6 : angle 2.23494 ( 6) link_BETA1-4 : bond 0.00444 ( 8) link_BETA1-4 : angle 2.74168 ( 24) link_NAG-ASN : bond 0.00721 ( 8) link_NAG-ASN : angle 3.25199 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 43 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7197 (mpp) REVERT: A 357 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8488 (m-30) REVERT: A 376 MET cc_start: 0.8721 (mmm) cc_final: 0.8431 (mmm) REVERT: A 717 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8160 (ptm-80) REVERT: B 57 MET cc_start: 0.4175 (mpp) cc_final: 0.3076 (mtm) REVERT: B 279 TYR cc_start: 0.8944 (m-80) cc_final: 0.8641 (m-80) REVERT: C 85 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6165 (p-80) REVERT: C 248 LEU cc_start: -0.1899 (OUTLIER) cc_final: -0.2177 (mt) REVERT: C 259 LEU cc_start: -0.2503 (OUTLIER) cc_final: -0.3053 (tp) outliers start: 42 outliers final: 30 residues processed: 79 average time/residue: 0.0908 time to fit residues: 11.6099 Evaluate side-chains 78 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.118692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.075444 restraints weight = 48627.003| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 5.43 r_work: 0.3083 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13212 Z= 0.160 Angle : 0.654 17.008 17931 Z= 0.314 Chirality : 0.046 0.346 2026 Planarity : 0.004 0.054 2325 Dihedral : 7.391 110.603 2186 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.19 % Allowed : 20.94 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1624 helix: 1.15 (0.28), residues: 360 sheet: -0.32 (0.24), residues: 430 loop : -1.25 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.012 0.001 TYR A 390 PHE 0.031 0.001 PHE A 121 TRP 0.024 0.001 TRP C 413 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00356 (13172) covalent geometry : angle 0.63410 (17831) SS BOND : bond 0.00171 ( 20) SS BOND : angle 0.59124 ( 40) hydrogen bonds : bond 0.02771 ( 473) hydrogen bonds : angle 4.89109 ( 1305) link_ALPHA1-3 : bond 0.01017 ( 2) link_ALPHA1-3 : angle 2.40750 ( 6) link_ALPHA1-6 : bond 0.01117 ( 2) link_ALPHA1-6 : angle 2.02536 ( 6) link_BETA1-4 : bond 0.00408 ( 8) link_BETA1-4 : angle 2.73829 ( 24) link_NAG-ASN : bond 0.00737 ( 8) link_NAG-ASN : angle 3.27183 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 42 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7224 (mpp) REVERT: A 312 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 357 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8871 (m-30) REVERT: A 376 MET cc_start: 0.8952 (mmm) cc_final: 0.8606 (mmm) REVERT: A 717 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8196 (ptm-80) REVERT: B 57 MET cc_start: 0.4077 (mpp) cc_final: 0.3118 (mtm) REVERT: B 279 TYR cc_start: 0.9163 (m-80) cc_final: 0.8821 (m-80) REVERT: C 85 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7195 (p-80) REVERT: C 242 GLU cc_start: 0.2649 (OUTLIER) cc_final: 0.2170 (tp30) REVERT: C 259 LEU cc_start: -0.1992 (OUTLIER) cc_final: -0.2826 (tp) outliers start: 44 outliers final: 33 residues processed: 79 average time/residue: 0.0874 time to fit residues: 11.0334 Evaluate side-chains 81 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 41 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.120905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078452 restraints weight = 48990.276| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 5.54 r_work: 0.3074 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13212 Z= 0.167 Angle : 0.669 16.393 17931 Z= 0.319 Chirality : 0.046 0.345 2026 Planarity : 0.004 0.054 2325 Dihedral : 7.334 110.808 2186 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 3.04 % Allowed : 21.01 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1624 helix: 1.14 (0.28), residues: 361 sheet: -0.31 (0.24), residues: 430 loop : -1.25 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 43 TYR 0.013 0.001 TYR A 390 PHE 0.033 0.001 PHE A 121 TRP 0.026 0.001 TRP C 413 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00371 (13172) covalent geometry : angle 0.64937 (17831) SS BOND : bond 0.00178 ( 20) SS BOND : angle 0.57809 ( 40) hydrogen bonds : bond 0.02777 ( 473) hydrogen bonds : angle 4.91106 ( 1305) link_ALPHA1-3 : bond 0.01024 ( 2) link_ALPHA1-3 : angle 2.39089 ( 6) link_ALPHA1-6 : bond 0.01131 ( 2) link_ALPHA1-6 : angle 1.82740 ( 6) link_BETA1-4 : bond 0.00407 ( 8) link_BETA1-4 : angle 2.73169 ( 24) link_NAG-ASN : bond 0.00739 ( 8) link_NAG-ASN : angle 3.25095 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 39 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7170 (mpp) REVERT: A 312 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8413 (tp) REVERT: A 357 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8896 (m-30) REVERT: A 376 MET cc_start: 0.8956 (mmm) cc_final: 0.8635 (mmm) REVERT: A 717 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8258 (ptm-80) REVERT: B 57 MET cc_start: 0.4395 (mpp) cc_final: 0.3397 (mtm) REVERT: B 279 TYR cc_start: 0.9173 (m-80) cc_final: 0.8822 (m-80) REVERT: C 85 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7076 (p-80) REVERT: C 242 GLU cc_start: 0.2601 (OUTLIER) cc_final: 0.2163 (tp30) REVERT: C 259 LEU cc_start: -0.2052 (OUTLIER) cc_final: -0.2856 (tp) outliers start: 42 outliers final: 33 residues processed: 74 average time/residue: 0.0956 time to fit residues: 11.4627 Evaluate side-chains 79 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 39 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 502 TRP Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 90 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 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 = 0.4491 r_free = 0.4491 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.076439 restraints weight = 48628.934| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 5.22 r_work: 0.3160 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13212 Z= 0.116 Angle : 0.636 17.301 17931 Z= 0.306 Chirality : 0.046 0.345 2026 Planarity : 0.004 0.053 2325 Dihedral : 7.169 109.560 2186 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 2.39 % Allowed : 21.67 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1624 helix: 1.20 (0.28), residues: 361 sheet: -0.28 (0.24), residues: 432 loop : -1.25 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 649 TYR 0.011 0.001 TYR B 308 PHE 0.029 0.001 PHE A 121 TRP 0.028 0.001 TRP C 413 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00253 (13172) covalent geometry : angle 0.61675 (17831) SS BOND : bond 0.00173 ( 20) SS BOND : angle 0.58054 ( 40) hydrogen bonds : bond 0.02651 ( 473) hydrogen bonds : angle 4.85096 ( 1305) link_ALPHA1-3 : bond 0.01090 ( 2) link_ALPHA1-3 : angle 2.30893 ( 6) link_ALPHA1-6 : bond 0.01142 ( 2) link_ALPHA1-6 : angle 1.53290 ( 6) link_BETA1-4 : bond 0.00412 ( 8) link_BETA1-4 : angle 2.68795 ( 24) link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 3.12136 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4675.99 seconds wall clock time: 80 minutes 10.96 seconds (4810.96 seconds total)