Starting phenix.real_space_refine on Thu Mar 5 22:58:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xgd_33186/03_2026/7xgd_33186.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 85 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 8488 2.51 5 N 2320 2.21 5 O 2546 1.98 5 H 12030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 12693 Classifications: {'peptide': 836} Modifications used: {'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 785} Chain breaks: 2 Chain: "B" Number of atoms: 12739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 12739 Classifications: {'peptide': 836} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 786} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 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 Time building chain proxies: 4.65, per 1000 atoms: 0.18 Number of scatterers: 25488 At special positions: 0 Unit cell: (145.26, 100.068, 138.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 2546 8.00 N 2320 7.00 C 8488 6.00 H 12030 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 670 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 105 " " NAG B1001 " - " ASN B 21 " " NAG B1002 " - " ASN B 105 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 967.4 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 35 sheets defined 17.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.126A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.748A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.642A pdb=" N ASN A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 314 through 321 removed outlier: 4.962A pdb=" N MET A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.631A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.045A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.527A pdb=" N ARG A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 506 through 510 removed outlier: 4.460A pdb=" N GLY A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.993A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 678 through 701 removed outlier: 4.094A pdb=" N SER A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.550A pdb=" N GLU B 20 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.993A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.655A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.644A pdb=" N ASN B 198 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.965A pdb=" N MET B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.640A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.903A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.747A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.547A pdb=" N ASP B 509 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 624 through 629 removed outlier: 4.006A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 701 removed outlier: 3.700A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 699 " --> pdb=" O PHE B 695 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.471A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 58 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 60 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 90 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 59 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.613A pdb=" N ILE A 51 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.511A pdb=" N THR A 177 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.638A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.564A pdb=" N TYR A 224 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.279A pdb=" N ARG A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA9, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.686A pdb=" N LYS A 309 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A 417 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 391 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 326 removed outlier: 8.125A pdb=" N PHE A 326 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL A 354 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 381 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 356 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 523 through 524 removed outlier: 3.627A pdb=" N THR A 494 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 552 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 587 through 590 Processing sheet with id=AB6, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.604A pdb=" N ASN A 789 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.078A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.078A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.446A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 58 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 90 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 24 through 25 removed outlier: 3.543A pdb=" N ILE B 51 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 209 removed outlier: 6.457A pdb=" N SER B 208 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.578A pdb=" N TYR B 224 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 239 through 241 removed outlier: 4.284A pdb=" N ARG B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC8, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.684A pdb=" N LYS B 309 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 358 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU B 393 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 360 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 8.161A pdb=" N PHE B 326 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL B 354 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU B 381 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY B 356 " --> pdb=" O GLU B 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AD2, first strand: chain 'B' and resid 523 through 524 removed outlier: 3.551A pdb=" N PHE B 493 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 567 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.722A pdb=" N LYS B 498 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 548 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 585 through 593 removed outlier: 5.042A pdb=" N VAL B 587 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 600 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 589 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 598 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 591 " --> pdb=" O GLN B 596 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 596 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 749 removed outlier: 4.178A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS B 776 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 789 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AD7, first strand: chain 'B' and resid 846 through 851 removed outlier: 4.093A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 846 through 851 removed outlier: 4.093A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 759 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: 7.59 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12030 1.03 - 1.23: 372 1.23 - 1.43: 5497 1.43 - 1.63: 7779 1.63 - 1.83: 132 Bond restraints: 25810 Sorted by residual: bond pdb=" C PRO A 581 " pdb=" N SER A 582 " ideal model delta sigma weight residual 1.328 1.348 -0.020 1.04e-02 9.25e+03 3.75e+00 bond pdb=" C ILE A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.71e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 25805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.01: 46019 8.01 - 16.03: 7 16.03 - 24.04: 0 24.04 - 32.05: 2 32.05 - 40.06: 10 Bond angle restraints: 46038 Sorted by residual: angle pdb=" C PRO B 293 " pdb=" CA PRO B 293 " pdb=" HA PRO B 293 " ideal model delta sigma weight residual 109.00 68.94 40.06 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C PRO A 299 " pdb=" CA PRO A 299 " pdb=" HA PRO A 299 " ideal model delta sigma weight residual 109.00 69.62 39.38 3.00e+00 1.11e-01 1.72e+02 angle pdb=" N PRO A 299 " pdb=" CA PRO A 299 " pdb=" HA PRO A 299 " ideal model delta sigma weight residual 110.00 74.04 35.96 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C ASN A 577 " pdb=" CA ASN A 577 " pdb=" HA ASN A 577 " ideal model delta sigma weight residual 109.00 73.09 35.91 3.00e+00 1.11e-01 1.43e+02 angle pdb=" N PRO B 293 " pdb=" CA PRO B 293 " pdb=" HA PRO B 293 " ideal model delta sigma weight residual 110.00 74.81 35.19 3.00e+00 1.11e-01 1.38e+02 ... (remaining 46033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11294 17.99 - 35.98: 936 35.98 - 53.97: 249 53.97 - 71.97: 53 71.97 - 89.96: 14 Dihedral angle restraints: 12546 sinusoidal: 6790 harmonic: 5756 Sorted by residual: dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -167.68 81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS B 234 " pdb=" SG CYS B 234 " pdb=" SG CYS B 246 " pdb=" CB CYS B 246 " ideal model delta sinusoidal sigma weight residual -86.00 -167.59 81.59 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A 294 " pdb=" SG CYS A 294 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual 93.00 166.56 -73.56 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 12543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1838 0.095 - 0.190: 168 0.190 - 0.285: 0 0.285 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN B 577 " pdb=" N ASN B 577 " pdb=" C ASN B 577 " pdb=" CB ASN B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASN A 577 " pdb=" N ASN A 577 " pdb=" C ASN A 577 " pdb=" CB ASN A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2007 not shown) Planarity restraints: 3884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 583 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A 584 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 544 " 0.022 2.00e-02 2.50e+03 1.19e-02 5.70e+00 pdb=" CG TRP A 544 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 544 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 544 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 544 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 544 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 544 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 544 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 544 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 544 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 544 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 544 " 0.010 2.00e-02 2.50e+03 pdb=" HE3 TRP A 544 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 544 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 544 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 544 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 298 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 299 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.028 5.00e-02 4.00e+02 ... (remaining 3881 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 780 2.09 - 2.72: 43676 2.72 - 3.35: 73662 3.35 - 3.97: 92950 3.97 - 4.60: 143267 Nonbonded interactions: 354335 Sorted by model distance: nonbonded pdb=" O THR A 324 " pdb=" H GLU A 352 " model vdw 1.467 2.450 nonbonded pdb=" O THR B 324 " pdb=" H GLU B 352 " model vdw 1.474 2.450 nonbonded pdb=" OE1 GLU A 826 " pdb=" H GLU A 826 " model vdw 1.536 2.450 nonbonded pdb=" OE1 GLU B 826 " pdb=" H GLU B 826 " model vdw 1.537 2.450 nonbonded pdb=" OE1 GLU A 507 " pdb=" HZ3 LYS A 568 " model vdw 1.541 2.450 ... (remaining 354330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or (resid 457 and (name N or name CA or name C or nam \ e O or name CB or name OG )) or (resid 458 and (name N or name CA or name C or n \ ame O or name CB or name SG )) or resid 459 through 579 or (resid 580 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 581 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or (resid 582 and (name N or name CA or name C or name O or name CB or name O \ G )) or (resid 583 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or resid 584 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.090 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13820 Z= 0.164 Angle : 0.719 12.502 18772 Z= 0.397 Chirality : 0.049 0.476 2010 Planarity : 0.005 0.068 2436 Dihedral : 13.044 89.957 5234 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.47 % Favored : 87.11 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.75 (0.19), residues: 1660 helix: -2.15 (0.36), residues: 159 sheet: -1.56 (0.30), residues: 268 loop : -1.98 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.023 0.002 TYR B 496 PHE 0.027 0.002 PHE A 90 TRP 0.038 0.002 TRP A 544 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00328 (13780) covalent geometry : angle 0.71269 (18688) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.41801 ( 72) hydrogen bonds : bond 0.19724 ( 304) hydrogen bonds : angle 8.94093 ( 759) link_NAG-ASN : bond 0.00251 ( 4) link_NAG-ASN : angle 2.20869 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 VAL cc_start: 0.7996 (t) cc_final: 0.7779 (t) REVERT: B 354 VAL cc_start: 0.7883 (t) cc_final: 0.7650 (t) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2345 time to fit residues: 41.4889 Evaluate side-chains 85 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 374 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.104629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.088370 restraints weight = 282924.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.091475 restraints weight = 142875.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.093313 restraints weight = 90532.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.094542 restraints weight = 66162.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.095258 restraints weight = 52426.939| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13820 Z= 0.171 Angle : 0.680 13.161 18772 Z= 0.364 Chirality : 0.049 0.486 2010 Planarity : 0.006 0.067 2436 Dihedral : 6.913 59.102 1936 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.93 % Favored : 87.65 % Rotamer: Outliers : 0.60 % Allowed : 4.89 % Favored : 94.50 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.85 (0.19), residues: 1660 helix: -1.91 (0.37), residues: 142 sheet: -1.93 (0.29), residues: 287 loop : -2.02 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.019 0.002 TYR A 688 PHE 0.021 0.002 PHE A 90 TRP 0.020 0.002 TRP B 544 HIS 0.006 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00362 (13780) covalent geometry : angle 0.67485 (18688) SS BOND : bond 0.00364 ( 36) SS BOND : angle 1.07263 ( 72) hydrogen bonds : bond 0.04872 ( 304) hydrogen bonds : angle 7.88094 ( 759) link_NAG-ASN : bond 0.00435 ( 4) link_NAG-ASN : angle 2.55184 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2425 (ptt) cc_final: 0.2113 (ptt) REVERT: A 354 VAL cc_start: 0.8030 (t) cc_final: 0.7800 (t) REVERT: B 354 VAL cc_start: 0.7895 (t) cc_final: 0.7661 (t) REVERT: B 496 TYR cc_start: 0.7892 (m-80) cc_final: 0.7289 (m-80) REVERT: B 525 ASP cc_start: 0.7239 (t0) cc_final: 0.6987 (t0) outliers start: 9 outliers final: 8 residues processed: 100 average time/residue: 0.2308 time to fit residues: 35.0050 Evaluate side-chains 90 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 48 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** 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 = 0.4553 r_free = 0.4553 target = 0.102387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.085937 restraints weight = 282834.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.088868 restraints weight = 144376.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.090724 restraints weight = 92579.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.091869 restraints weight = 67779.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.092546 restraints weight = 54275.934| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13820 Z= 0.243 Angle : 0.727 11.739 18772 Z= 0.387 Chirality : 0.049 0.487 2010 Planarity : 0.006 0.064 2436 Dihedral : 7.121 57.550 1936 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.70 % Favored : 84.88 % Rotamer: Outliers : 1.21 % Allowed : 8.04 % Favored : 90.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.19), residues: 1660 helix: -2.00 (0.36), residues: 142 sheet: -2.30 (0.28), residues: 297 loop : -2.18 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.035 0.002 TYR A 83 PHE 0.022 0.002 PHE A 90 TRP 0.027 0.002 TRP B 544 HIS 0.005 0.002 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00503 (13780) covalent geometry : angle 0.72159 (18688) SS BOND : bond 0.00485 ( 36) SS BOND : angle 1.22606 ( 72) hydrogen bonds : bond 0.04892 ( 304) hydrogen bonds : angle 7.80897 ( 759) link_NAG-ASN : bond 0.00683 ( 4) link_NAG-ASN : angle 2.64458 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2903 (ptt) cc_final: 0.2425 (ptt) REVERT: A 345 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: B 345 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6300 (mp0) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.2030 time to fit residues: 33.6667 Evaluate side-chains 99 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.102540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.086293 restraints weight = 282354.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.089785 restraints weight = 164229.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.090477 restraints weight = 100914.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.091206 restraints weight = 79687.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.091478 restraints weight = 70922.138| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13820 Z= 0.183 Angle : 0.668 11.833 18772 Z= 0.356 Chirality : 0.049 0.485 2010 Planarity : 0.006 0.064 2436 Dihedral : 6.996 59.099 1936 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.89 % Favored : 86.69 % Rotamer: Outliers : 1.21 % Allowed : 10.12 % Favored : 88.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.19), residues: 1660 helix: -1.92 (0.37), residues: 143 sheet: -2.31 (0.27), residues: 296 loop : -2.13 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.023 0.002 TYR B 496 PHE 0.014 0.002 PHE B 82 TRP 0.023 0.002 TRP B 544 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00381 (13780) covalent geometry : angle 0.66415 (18688) SS BOND : bond 0.00394 ( 36) SS BOND : angle 0.97643 ( 72) hydrogen bonds : bond 0.04054 ( 304) hydrogen bonds : angle 7.48635 ( 759) link_NAG-ASN : bond 0.00367 ( 4) link_NAG-ASN : angle 2.42668 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2759 (ptt) cc_final: 0.2303 (ptt) REVERT: A 345 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: B 345 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: B 496 TYR cc_start: 0.7858 (m-80) cc_final: 0.7411 (m-80) REVERT: B 525 ASP cc_start: 0.7308 (t0) cc_final: 0.7098 (t0) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.1804 time to fit residues: 30.8003 Evaluate side-chains 99 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 162 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** 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 = 0.4556 r_free = 0.4556 target = 0.102421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.086106 restraints weight = 281685.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.089159 restraints weight = 143141.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.091052 restraints weight = 91448.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.092158 restraints weight = 66469.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.092922 restraints weight = 53194.718| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13820 Z= 0.160 Angle : 0.642 11.130 18772 Z= 0.339 Chirality : 0.049 0.480 2010 Planarity : 0.005 0.060 2436 Dihedral : 6.796 59.096 1936 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.13 % Favored : 86.45 % Rotamer: Outliers : 1.81 % Allowed : 10.66 % Favored : 87.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.19), residues: 1660 helix: -1.76 (0.39), residues: 137 sheet: -2.30 (0.28), residues: 297 loop : -2.09 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 222 TYR 0.025 0.002 TYR B 496 PHE 0.017 0.002 PHE A 82 TRP 0.020 0.002 TRP B 544 HIS 0.005 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00340 (13780) covalent geometry : angle 0.63810 (18688) SS BOND : bond 0.00333 ( 36) SS BOND : angle 0.92911 ( 72) hydrogen bonds : bond 0.03661 ( 304) hydrogen bonds : angle 7.10363 ( 759) link_NAG-ASN : bond 0.00390 ( 4) link_NAG-ASN : angle 2.32477 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2141 (ptt) cc_final: 0.1673 (ptt) REVERT: A 345 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: B 345 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5941 (mp0) REVERT: B 525 ASP cc_start: 0.7254 (t0) cc_final: 0.7053 (t0) outliers start: 27 outliers final: 20 residues processed: 111 average time/residue: 0.1890 time to fit residues: 33.9550 Evaluate side-chains 105 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** 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 = 0.4456 r_free = 0.4456 target = 0.099268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.082463 restraints weight = 284111.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.085400 restraints weight = 141512.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.087273 restraints weight = 89914.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.088386 restraints weight = 65520.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.089038 restraints weight = 52523.233| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 13820 Z= 0.300 Angle : 0.783 10.945 18772 Z= 0.417 Chirality : 0.050 0.485 2010 Planarity : 0.007 0.069 2436 Dihedral : 7.254 56.356 1936 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 34.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 15.48 % Favored : 84.10 % Rotamer: Outliers : 2.41 % Allowed : 11.06 % Favored : 86.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 1.04 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.19), residues: 1660 helix: -2.03 (0.37), residues: 148 sheet: -2.82 (0.26), residues: 299 loop : -2.37 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 222 TYR 0.037 0.003 TYR B 83 PHE 0.021 0.003 PHE B 82 TRP 0.027 0.003 TRP B 544 HIS 0.011 0.002 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00622 (13780) covalent geometry : angle 0.77792 (18688) SS BOND : bond 0.00548 ( 36) SS BOND : angle 1.21413 ( 72) hydrogen bonds : bond 0.04555 ( 304) hydrogen bonds : angle 7.62619 ( 759) link_NAG-ASN : bond 0.00740 ( 4) link_NAG-ASN : angle 2.69843 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2365 (ptt) cc_final: 0.1859 (ptt) REVERT: A 345 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6022 (mp0) REVERT: A 458 CYS cc_start: 0.5078 (OUTLIER) cc_final: 0.4671 (p) REVERT: B 345 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5976 (mp0) outliers start: 36 outliers final: 32 residues processed: 115 average time/residue: 0.1786 time to fit residues: 33.8226 Evaluate side-chains 117 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 164 optimal weight: 9.9990 chunk 157 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** 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 = 0.4435 r_free = 0.4435 target = 0.098343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.079475 restraints weight = 243506.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.082834 restraints weight = 120478.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.084936 restraints weight = 75311.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.086255 restraints weight = 54117.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.087069 restraints weight = 42728.854| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13820 Z= 0.147 Angle : 0.653 11.994 18772 Z= 0.346 Chirality : 0.049 0.483 2010 Planarity : 0.006 0.065 2436 Dihedral : 6.913 59.973 1936 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.35 % Favored : 87.23 % Rotamer: Outliers : 1.94 % Allowed : 12.00 % Favored : 86.06 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.19), residues: 1660 helix: -1.79 (0.39), residues: 142 sheet: -2.58 (0.27), residues: 296 loop : -2.20 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 481 TYR 0.019 0.002 TYR A 835 PHE 0.014 0.002 PHE B 82 TRP 0.022 0.002 TRP B 544 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00318 (13780) covalent geometry : angle 0.65053 (18688) SS BOND : bond 0.00344 ( 36) SS BOND : angle 0.81478 ( 72) hydrogen bonds : bond 0.03545 ( 304) hydrogen bonds : angle 7.07521 ( 759) link_NAG-ASN : bond 0.00422 ( 4) link_NAG-ASN : angle 2.16791 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2427 (ptt) cc_final: 0.2018 (ptt) REVERT: A 184 MET cc_start: 0.4259 (mpp) cc_final: 0.3297 (mpp) REVERT: A 345 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 458 CYS cc_start: 0.5226 (OUTLIER) cc_final: 0.4803 (p) REVERT: A 558 MET cc_start: 0.3481 (ptt) cc_final: 0.3219 (ptt) REVERT: B 83 TYR cc_start: 0.8298 (t80) cc_final: 0.8048 (t80) REVERT: B 345 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6242 (mp0) outliers start: 29 outliers final: 23 residues processed: 114 average time/residue: 0.2054 time to fit residues: 37.7143 Evaluate side-chains 108 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.097679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.078835 restraints weight = 240253.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.082134 restraints weight = 119191.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.084221 restraints weight = 74725.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.085523 restraints weight = 53585.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.086271 restraints weight = 42411.642| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13820 Z= 0.178 Angle : 0.661 11.501 18772 Z= 0.349 Chirality : 0.049 0.483 2010 Planarity : 0.006 0.066 2436 Dihedral : 6.883 59.915 1936 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.92 % Favored : 85.66 % Rotamer: Outliers : 2.35 % Allowed : 12.00 % Favored : 85.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.19), residues: 1660 helix: -1.80 (0.40), residues: 142 sheet: -2.60 (0.27), residues: 296 loop : -2.21 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 222 TYR 0.013 0.002 TYR B 547 PHE 0.018 0.002 PHE B 82 TRP 0.021 0.002 TRP B 544 HIS 0.004 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00378 (13780) covalent geometry : angle 0.65652 (18688) SS BOND : bond 0.00411 ( 36) SS BOND : angle 1.01065 ( 72) hydrogen bonds : bond 0.03636 ( 304) hydrogen bonds : angle 7.01855 ( 759) link_NAG-ASN : bond 0.00501 ( 4) link_NAG-ASN : angle 2.26300 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2569 (ptt) cc_final: 0.2082 (ptt) REVERT: A 345 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 458 CYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4735 (p) REVERT: B 345 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: B 688 TYR cc_start: 0.7505 (t80) cc_final: 0.7174 (m-80) outliers start: 35 outliers final: 28 residues processed: 114 average time/residue: 0.2065 time to fit residues: 37.1466 Evaluate side-chains 113 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** 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 = 0.4439 r_free = 0.4439 target = 0.098658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.079840 restraints weight = 242427.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.083276 restraints weight = 119697.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.085408 restraints weight = 74399.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.086747 restraints weight = 53153.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.087524 restraints weight = 41775.788| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13820 Z= 0.127 Angle : 0.626 11.620 18772 Z= 0.331 Chirality : 0.049 0.482 2010 Planarity : 0.005 0.067 2436 Dihedral : 6.662 58.732 1936 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.47 % Favored : 87.11 % Rotamer: Outliers : 1.88 % Allowed : 12.47 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.20), residues: 1660 helix: -1.43 (0.42), residues: 134 sheet: -2.41 (0.27), residues: 286 loop : -2.16 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.013 0.002 TYR A 688 PHE 0.019 0.001 PHE B 82 TRP 0.030 0.002 TRP A 810 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00281 (13780) covalent geometry : angle 0.62255 (18688) SS BOND : bond 0.00331 ( 36) SS BOND : angle 0.92404 ( 72) hydrogen bonds : bond 0.03277 ( 304) hydrogen bonds : angle 6.80028 ( 759) link_NAG-ASN : bond 0.00386 ( 4) link_NAG-ASN : angle 2.05861 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2435 (ptt) cc_final: 0.1979 (ptt) REVERT: A 345 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: A 458 CYS cc_start: 0.4904 (OUTLIER) cc_final: 0.4529 (p) REVERT: B 345 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: B 521 MET cc_start: 0.8826 (mmm) cc_final: 0.8606 (mmm) REVERT: B 688 TYR cc_start: 0.7621 (t80) cc_final: 0.7400 (m-80) outliers start: 28 outliers final: 23 residues processed: 110 average time/residue: 0.1937 time to fit residues: 33.8645 Evaluate side-chains 111 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 835 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 102 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.099333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.080747 restraints weight = 243825.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.084253 restraints weight = 118755.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.086413 restraints weight = 73367.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.087710 restraints weight = 52076.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.088560 restraints weight = 40930.850| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13820 Z= 0.115 Angle : 0.609 11.344 18772 Z= 0.320 Chirality : 0.049 0.481 2010 Planarity : 0.005 0.066 2436 Dihedral : 6.366 54.902 1936 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.17 % Favored : 87.41 % Rotamer: Outliers : 1.81 % Allowed : 12.60 % Favored : 85.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.90 (0.20), residues: 1660 helix: -1.22 (0.43), residues: 134 sheet: -2.23 (0.28), residues: 286 loop : -2.08 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 222 TYR 0.022 0.002 TYR B 83 PHE 0.022 0.001 PHE B 82 TRP 0.014 0.001 TRP A 810 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00257 (13780) covalent geometry : angle 0.60623 (18688) SS BOND : bond 0.00286 ( 36) SS BOND : angle 0.84381 ( 72) hydrogen bonds : bond 0.03196 ( 304) hydrogen bonds : angle 6.55552 ( 759) link_NAG-ASN : bond 0.00288 ( 4) link_NAG-ASN : angle 1.96517 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.2218 (ptt) cc_final: 0.1764 (ptt) REVERT: A 345 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: A 458 CYS cc_start: 0.4690 (OUTLIER) cc_final: 0.4336 (p) REVERT: A 688 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: B 345 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: B 688 TYR cc_start: 0.7506 (t80) cc_final: 0.7241 (m-80) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.1940 time to fit residues: 32.6425 Evaluate side-chains 106 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 688 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 151 optimal weight: 0.0870 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.099717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.080979 restraints weight = 243528.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.084468 restraints weight = 118246.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.086643 restraints weight = 73265.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.087976 restraints weight = 52163.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.088808 restraints weight = 40941.153| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13820 Z= 0.115 Angle : 0.608 11.253 18772 Z= 0.318 Chirality : 0.049 0.478 2010 Planarity : 0.005 0.066 2436 Dihedral : 6.278 54.169 1936 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.93 % Favored : 87.65 % Rotamer: Outliers : 1.74 % Allowed : 12.67 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.86 (0.20), residues: 1660 helix: -1.19 (0.43), residues: 134 sheet: -2.17 (0.28), residues: 286 loop : -2.06 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.025 0.001 TYR A 688 PHE 0.018 0.001 PHE B 82 TRP 0.014 0.001 TRP B 544 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00258 (13780) covalent geometry : angle 0.60510 (18688) SS BOND : bond 0.00280 ( 36) SS BOND : angle 0.87201 ( 72) hydrogen bonds : bond 0.03116 ( 304) hydrogen bonds : angle 6.49041 ( 759) link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 1.95665 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5075.22 seconds wall clock time: 87 minutes 14.57 seconds (5234.57 seconds total)