Starting phenix.real_space_refine on Thu Aug 6 08:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pig_71666/08_2026/9pig_71666.map" } resolution = 2.79 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 9116 2.51 5 N 2346 2.21 5 O 2482 1.98 5 H 4 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6737 Classifications: {'peptide': 860} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 822} Chain breaks: 1 Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 209 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain breaks: 1 Chain: "B" Number of atoms: 6737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6737 Classifications: {'peptide': 860} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 822} Chain breaks: 1 Chain: "C" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 209 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {' NA': 1, 'ATP': 1, 'BL1': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {' NA': 1, 'ATP': 1, 'BL1': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.23 Number of scatterers: 14038 At special positions: 0 Unit cell: (114.38, 104.06, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 6 15.00 Na 2 11.00 O 2482 8.00 N 2346 7.00 C 9116 6.00 H 4 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " 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 A1102 " - " ASN A 426 " " NAG B1102 " - " ASN B 426 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 611.0 milliseconds 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 2 sheets defined 61.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 167 through 192 removed outlier: 3.724A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 214 through 249 removed outlier: 3.835A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.925A pdb=" N ARG A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 removed outlier: 3.505A pdb=" N LEU A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.039A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.677A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 394 removed outlier: 3.796A pdb=" N ILE A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.509A pdb=" N LEU A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 453 through 485 removed outlier: 3.861A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.654A pdb=" N PHE A 495 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 496 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS A 497 " --> pdb=" O PHE A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 497' Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.703A pdb=" N TYR A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.767A pdb=" N PHE A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 585 removed outlier: 3.598A pdb=" N ALA A 570 " --> pdb=" O ASN A 566 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 606 removed outlier: 3.602A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.923A pdb=" N TYR A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 removed outlier: 3.649A pdb=" N VAL A 634 " --> pdb=" O LEU A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.590A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 removed outlier: 4.152A pdb=" N VAL A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 Processing helix chain 'A' and resid 716 through 728 removed outlier: 3.843A pdb=" N ILE A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 727 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 767 removed outlier: 3.839A pdb=" N GLU A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.852A pdb=" N SER A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 removed outlier: 3.623A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 904 through 913 removed outlier: 3.540A pdb=" N PHE A 911 " --> pdb=" O HIS A 907 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.707A pdb=" N PHE A 918 " --> pdb=" O ILE A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 950 through 967 removed outlier: 3.635A pdb=" N GLN A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.851A pdb=" N SER A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.503A pdb=" N ASN B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 159 through 190 removed outlier: 3.730A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N VAL B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.545A pdb=" N LEU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 249 removed outlier: 3.730A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.975A pdb=" N ARG B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 removed outlier: 3.556A pdb=" N SER B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 339 through 348 removed outlier: 4.205A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 366 through 393 removed outlier: 3.873A pdb=" N ILE B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix removed outlier: 3.684A pdb=" N LEU B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 453 through 485 removed outlier: 3.943A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 476 " --> pdb=" O CYS B 472 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.573A pdb=" N PHE B 495 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 496 " --> pdb=" O GLY B 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 496' Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.714A pdb=" N TYR B 513 " --> pdb=" O TYR B 509 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 521 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 3.506A pdb=" N ASN B 534 " --> pdb=" O PRO B 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 540 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.560A pdb=" N GLY B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 606 removed outlier: 3.594A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 591 " --> pdb=" O TRP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 630 removed outlier: 3.626A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 621 " --> pdb=" O GLN B 617 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 removed outlier: 3.672A pdb=" N VAL B 634 " --> pdb=" O LEU B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.654A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 666 removed outlier: 4.063A pdb=" N VAL B 659 " --> pdb=" O ARG B 655 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 666 " --> pdb=" O VAL B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.545A pdb=" N LEU B 700 " --> pdb=" O HIS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 728 removed outlier: 3.691A pdb=" N GLN B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 723 " --> pdb=" O ARG B 719 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 767 removed outlier: 3.874A pdb=" N VAL B 754 " --> pdb=" O HIS B 750 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 757 " --> pdb=" O THR B 753 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 824 removed outlier: 3.629A pdb=" N SER B 824 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 851 removed outlier: 3.631A pdb=" N ILE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Proline residue: B 847 - end of helix removed outlier: 3.505A pdb=" N GLY B 851 " --> pdb=" O PRO B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 removed outlier: 6.807A pdb=" N ARG B 855 " --> pdb=" O ARG B 852 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 857 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.561A pdb=" N PHE B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 913 removed outlier: 3.575A pdb=" N PHE B 911 " --> pdb=" O HIS B 907 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 919 Processing helix chain 'B' and resid 926 through 934 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 950 through 967 removed outlier: 3.766A pdb=" N GLN B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.589A pdb=" N LEU B 994 " --> pdb=" O TYR B 990 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 995 " --> pdb=" O MET B 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing sheet with id=AA1, first strand: chain 'A' and resid 708 through 714 removed outlier: 6.520A pdb=" N LEU A 646 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLY A 741 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LEU A 648 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 972 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 976 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 831 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 864 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 833 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY A 866 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 861 " --> pdb=" O GLU A 892 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N HIS A 894 " --> pdb=" O ILE A 861 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 863 " --> pdb=" O HIS A 894 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 896 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 865 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 714 removed outlier: 6.747A pdb=" N CYS B 645 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY B 675 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 647 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY B 741 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 972 " --> pdb=" O THR B 830 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 976 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 861 " --> pdb=" O GLU B 892 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N HIS B 894 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 863 " --> pdb=" O HIS B 894 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.07: 4 1.07 - 1.29: 2178 1.29 - 1.51: 6327 1.51 - 1.73: 5747 1.73 - 1.95: 124 Bond restraints: 14380 Sorted by residual: bond pdb=" CAO BL1 B1103 " pdb=" SAX BL1 B1103 " ideal model delta sigma weight residual 1.791 1.946 -0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" CAO BL1 A1103 " pdb=" SAX BL1 A1103 " ideal model delta sigma weight residual 1.791 1.944 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" O3A ATP B1104 " pdb=" PB ATP B1104 " ideal model delta sigma weight residual 1.592 1.668 -0.076 1.10e-02 8.26e+03 4.74e+01 bond pdb=" O3A ATP A1104 " pdb=" PB ATP A1104 " ideal model delta sigma weight residual 1.592 1.667 -0.075 1.10e-02 8.26e+03 4.67e+01 bond pdb=" C3' ATP A1104 " pdb=" O3' ATP A1104 " ideal model delta sigma weight residual 1.423 1.356 0.067 1.10e-02 8.26e+03 3.71e+01 ... (remaining 14375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 19483 4.60 - 9.20: 51 9.20 - 13.81: 4 13.81 - 18.41: 2 18.41 - 23.01: 8 Bond angle restraints: 19548 Sorted by residual: angle pdb=" O3A ATP B1104 " pdb=" PB ATP B1104 " pdb=" O3B ATP B1104 " ideal model delta sigma weight residual 101.57 124.58 -23.01 1.54e+00 4.24e-01 2.24e+02 angle pdb=" O3A ATP A1104 " pdb=" PB ATP A1104 " pdb=" O3B ATP A1104 " ideal model delta sigma weight residual 101.57 123.63 -22.06 1.54e+00 4.24e-01 2.06e+02 angle pdb=" O1G ATP B1104 " pdb=" PG ATP B1104 " pdb=" O3B ATP B1104 " ideal model delta sigma weight residual 110.47 129.91 -19.44 1.64e+00 3.70e-01 1.40e+02 angle pdb=" O1G ATP A1104 " pdb=" PG ATP A1104 " pdb=" O3B ATP A1104 " ideal model delta sigma weight residual 110.47 129.69 -19.22 1.64e+00 3.70e-01 1.37e+02 angle pdb=" C5' ATP A1104 " pdb=" O5' ATP A1104 " pdb=" PA ATP A1104 " ideal model delta sigma weight residual 121.27 131.47 -10.20 1.00e+00 1.00e+00 1.04e+02 ... (remaining 19543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7636 17.85 - 35.70: 651 35.70 - 53.54: 160 53.54 - 71.39: 67 71.39 - 89.24: 6 Dihedral angle restraints: 8520 sinusoidal: 3436 harmonic: 5084 Sorted by residual: dihedral pdb=" CB CYS B 430 " pdb=" SG CYS B 430 " pdb=" SG CYS B 436 " pdb=" CB CYS B 436 " ideal model delta sinusoidal sigma weight residual 93.00 175.95 -82.95 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 175.01 -82.01 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" SG CYS A 430 " pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" CA CYS A 436 " ideal model delta sinusoidal sigma weight residual 79.00 8.52 70.48 1 2.00e+01 2.50e-03 1.60e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1960 0.062 - 0.124: 230 0.124 - 0.186: 17 0.186 - 0.248: 7 0.248 - 0.310: 2 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CAI BL1 A1103 " pdb=" CAF BL1 A1103 " pdb=" CAP BL1 A1103 " pdb=" NAT BL1 A1103 " both_signs ideal model delta sigma weight residual False 2.74 3.05 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CAI BL1 B1103 " pdb=" CAF BL1 B1103 " pdb=" CAP BL1 B1103 " pdb=" NAT BL1 B1103 " both_signs ideal model delta sigma weight residual False 2.74 3.04 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA SER B 967 " pdb=" N SER B 967 " pdb=" C SER B 967 " pdb=" CB SER B 967 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2213 not shown) Planarity restraints: 2432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 685 " 0.247 9.50e-02 1.11e+02 1.11e-01 7.51e+00 pdb=" NE ARG A 685 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 685 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 685 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 685 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 894 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C HIS A 894 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS A 894 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 895 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 306 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 307 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.023 5.00e-02 4.00e+02 ... (remaining 2429 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.69: 248 2.69 - 3.17: 10845 3.17 - 3.65: 15138 3.65 - 4.12: 20563 4.12 - 4.60: 33511 Nonbonded interactions: 80305 Sorted by model distance: nonbonded pdb=" O LEU B 148 " pdb="NA NA B1101 " model vdw 2.216 2.350 nonbonded pdb=" O LEU A 148 " pdb="NA NA A1101 " model vdw 2.239 2.350 nonbonded pdb=" O ASN A 949 " pdb=" OG SER A 953 " model vdw 2.241 2.800 nonbonded pdb=" OD1 ASP B 922 " pdb=" N GLY B 923 " model vdw 2.245 2.950 nonbonded pdb=" O VAL A 662 " pdb=" OG1 THR A 666 " model vdw 2.265 2.800 ... (remaining 80300 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 14382 Z= 0.376 Angle : 0.862 23.008 19560 Z= 0.514 Chirality : 0.044 0.310 2216 Planarity : 0.004 0.111 2430 Dihedral : 14.923 89.240 5248 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.20), residues: 1754 helix: -1.06 (0.17), residues: 976 sheet: 0.61 (0.47), residues: 140 loop : -1.92 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 852 TYR 0.019 0.001 TYR A 156 PHE 0.012 0.001 PHE B 427 TRP 0.011 0.001 TRP A 587 HIS 0.003 0.001 HIS B 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.38 (14376) covalent geometry : angle 0.86122 / 0.51 (19546) SS BOND : bond 0.00081 / 0.04 ( 4) SS BOND : angle 1.36285 / 0.66 ( 8) hydrogen bonds : bond 0.29331 / 19.63 ( 651) hydrogen bonds : angle 7.05050 / 5.25 ( 1890) link_NAG-ASN : bond 0.00048 / 0.03 ( 2) link_NAG-ASN : angle 1.84639 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.563 Fit side-chains REVERT: A 635 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8393 (mm-30) REVERT: A 685 ARG cc_start: 0.6097 (mtp180) cc_final: 0.5450 (tmt170) REVERT: A 694 ASN cc_start: 0.8207 (m-40) cc_final: 0.7753 (m-40) REVERT: A 701 ASN cc_start: 0.8505 (t0) cc_final: 0.8228 (t0) REVERT: A 719 ARG cc_start: 0.8962 (mtm-85) cc_final: 0.8495 (mpt180) REVERT: A 872 MET cc_start: 0.7657 (mtp) cc_final: 0.7090 (mtm) REVERT: A 877 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7956 (mmtt) REVERT: A 881 SER cc_start: 0.8905 (t) cc_final: 0.8609 (m) REVERT: A 898 ASP cc_start: 0.6495 (m-30) cc_final: 0.6245 (m-30) REVERT: A 925 LYS cc_start: 0.8130 (mptt) cc_final: 0.7820 (tppt) REVERT: A 1002 ARG cc_start: 0.8559 (mmt180) cc_final: 0.8127 (mmp80) REVERT: B 259 ASP cc_start: 0.8250 (m-30) cc_final: 0.8030 (m-30) REVERT: B 524 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7612 (tm-30) REVERT: B 607 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7823 (mtpp) REVERT: B 635 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8243 (mm-30) REVERT: B 685 ARG cc_start: 0.6008 (mtp180) cc_final: 0.5391 (tmt170) REVERT: B 690 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8294 (mm-40) REVERT: B 719 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8399 (mpt180) REVERT: B 877 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8156 (mmtt) REVERT: B 898 ASP cc_start: 0.6377 (m-30) cc_final: 0.6150 (m-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.6900 time to fit residues: 126.7255 Evaluate side-chains 154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 165 GLN A 286 GLN A 299 ASN A 328 ASN A 359 ASN A 481 GLN A 644 GLN A 684 GLN A 701 ASN A 762 HIS A 817 GLN A 956 GLN B 149 ASN B 165 GLN B 234 HIS B 299 ASN B 328 ASN B 481 GLN B 644 GLN B 684 GLN B 701 ASN B 745 ASN B 817 GLN B 900 ASN B 956 GLN B1012 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103244 restraints weight = 16222.050| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.16 r_work: 0.2929 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14382 Z= 0.124 Angle : 0.493 5.061 19560 Z= 0.267 Chirality : 0.039 0.141 2216 Planarity : 0.004 0.034 2430 Dihedral : 8.967 84.068 2056 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.07 % Allowed : 12.25 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1754 helix: 0.14 (0.17), residues: 984 sheet: 0.73 (0.45), residues: 142 loop : -1.88 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 775 TYR 0.014 0.001 TYR A 300 PHE 0.014 0.001 PHE B 325 TRP 0.010 0.001 TRP B 699 HIS 0.003 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14376) covalent geometry : angle 0.48864 / 0.27 (19546) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 2.71038 / 1.31 ( 8) hydrogen bonds : bond 0.06999 / 4.63 ( 651) hydrogen bonds : angle 4.27865 / 3.17 ( 1890) link_NAG-ASN : bond 0.00154 / 0.08 ( 2) link_NAG-ASN : angle 2.15117 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.511 Fit side-chains REVERT: A 635 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 671 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8680 (tp) REVERT: A 685 ARG cc_start: 0.6041 (mtp180) cc_final: 0.5405 (tmt170) REVERT: A 694 ASN cc_start: 0.7407 (m-40) cc_final: 0.6923 (m-40) REVERT: A 719 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7542 (mpt180) REVERT: A 872 MET cc_start: 0.6932 (mtp) cc_final: 0.6511 (mtm) REVERT: A 877 LYS cc_start: 0.7480 (mmtp) cc_final: 0.7111 (mmpt) REVERT: A 898 ASP cc_start: 0.6649 (m-30) cc_final: 0.6412 (m-30) REVERT: A 925 LYS cc_start: 0.7895 (mptt) cc_final: 0.7681 (tppt) REVERT: A 1002 ARG cc_start: 0.8255 (mmt180) cc_final: 0.7628 (mmp80) REVERT: B 257 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 445 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: B 524 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7281 (tm-30) REVERT: B 583 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7146 (mp) REVERT: B 607 LYS cc_start: 0.7491 (mtpt) cc_final: 0.7199 (mtpp) REVERT: B 635 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7662 (mm-30) REVERT: B 671 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 685 ARG cc_start: 0.6114 (mtp180) cc_final: 0.5344 (tmt170) REVERT: B 694 ASN cc_start: 0.7499 (m-40) cc_final: 0.7007 (m-40) REVERT: B 719 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7525 (mpt180) REVERT: B 745 ASN cc_start: 0.8168 (p0) cc_final: 0.7950 (p0) REVERT: B 877 LYS cc_start: 0.7378 (mmtp) cc_final: 0.7017 (mmpt) REVERT: B 898 ASP cc_start: 0.6577 (m-30) cc_final: 0.6347 (m-30) REVERT: B 982 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7087 (mtpt) REVERT: B 1002 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7355 (mpp80) outliers start: 31 outliers final: 8 residues processed: 165 average time/residue: 0.6581 time to fit residues: 118.1641 Evaluate side-chains 152 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 982 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 701 ASN B 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103183 restraints weight = 16328.017| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.18 r_work: 0.2944 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14382 Z= 0.104 Angle : 0.429 3.808 19560 Z= 0.231 Chirality : 0.038 0.140 2216 Planarity : 0.003 0.034 2430 Dihedral : 8.803 88.953 2056 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.87 % Allowed : 12.78 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1754 helix: 0.75 (0.17), residues: 984 sheet: 0.83 (0.45), residues: 142 loop : -1.80 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 775 TYR 0.010 0.001 TYR A 300 PHE 0.010 0.001 PHE B 380 TRP 0.009 0.001 TRP B 587 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (14376) covalent geometry : angle 0.42727 / 0.23 (19546) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 1.41660 / 0.69 ( 8) hydrogen bonds : bond 0.06053 / 4.00 ( 651) hydrogen bonds : angle 3.92173 / 2.91 ( 1890) link_NAG-ASN : bond 0.00099 / 0.05 ( 2) link_NAG-ASN : angle 1.88115 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.465 Fit side-chains REVERT: A 445 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: A 635 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7783 (mm-30) REVERT: A 671 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 685 ARG cc_start: 0.5953 (mtp180) cc_final: 0.5367 (tmt170) REVERT: A 694 ASN cc_start: 0.7446 (m-40) cc_final: 0.6961 (m-40) REVERT: A 701 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (m110) REVERT: A 719 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7519 (mpt180) REVERT: A 872 MET cc_start: 0.6832 (mtp) cc_final: 0.6445 (mtm) REVERT: A 877 LYS cc_start: 0.7521 (mmtp) cc_final: 0.7213 (mmtt) REVERT: A 898 ASP cc_start: 0.6612 (m-30) cc_final: 0.6364 (m-30) REVERT: A 925 LYS cc_start: 0.7864 (mptt) cc_final: 0.7655 (tppt) REVERT: A 1002 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7615 (mmp80) REVERT: B 321 ARG cc_start: 0.6828 (mmt180) cc_final: 0.6515 (mmt-90) REVERT: B 445 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: B 524 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7308 (tm-30) REVERT: B 583 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7188 (mp) REVERT: B 607 LYS cc_start: 0.7390 (mtpt) cc_final: 0.7116 (mtpp) REVERT: B 635 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7665 (mm-30) REVERT: B 685 ARG cc_start: 0.6049 (mtp180) cc_final: 0.5328 (tmt170) REVERT: B 694 ASN cc_start: 0.7526 (m-40) cc_final: 0.7027 (m-40) REVERT: B 719 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7563 (mpt180) REVERT: B 877 LYS cc_start: 0.7398 (mmtp) cc_final: 0.7102 (mmtt) REVERT: B 898 ASP cc_start: 0.6651 (m-30) cc_final: 0.6421 (m-30) REVERT: B 909 LYS cc_start: 0.7196 (tttt) cc_final: 0.6891 (ttmm) REVERT: B 982 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7124 (mtpt) outliers start: 28 outliers final: 13 residues processed: 158 average time/residue: 0.6791 time to fit residues: 116.4295 Evaluate side-chains 158 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 982 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 170 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 299 ASN A 900 ASN B 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104616 restraints weight = 16253.788| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.18 r_work: 0.2970 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14382 Z= 0.087 Angle : 0.404 4.898 19560 Z= 0.217 Chirality : 0.038 0.137 2216 Planarity : 0.003 0.031 2430 Dihedral : 8.113 81.660 2056 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 13.25 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1754 helix: 1.12 (0.18), residues: 984 sheet: 0.90 (0.45), residues: 146 loop : -1.71 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.007 0.001 TYR B 769 PHE 0.012 0.001 PHE A 325 TRP 0.009 0.001 TRP B 587 HIS 0.002 0.001 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (14376) covalent geometry : angle 0.39965 / 0.22 (19546) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 2.45197 / 1.19 ( 8) hydrogen bonds : bond 0.04998 / 3.29 ( 651) hydrogen bonds : angle 3.70561 / 2.74 ( 1890) link_NAG-ASN : bond 0.00095 / 0.05 ( 2) link_NAG-ASN : angle 1.90890 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.508 Fit side-chains REVERT: A 407 ASP cc_start: 0.7957 (t70) cc_final: 0.6930 (t0) REVERT: A 445 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: A 635 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7821 (mm-30) REVERT: A 671 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8637 (tp) REVERT: A 685 ARG cc_start: 0.5905 (mtp180) cc_final: 0.5340 (tmt170) REVERT: A 694 ASN cc_start: 0.7428 (m-40) cc_final: 0.6963 (m-40) REVERT: A 719 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7466 (mpt180) REVERT: A 872 MET cc_start: 0.6852 (mtp) cc_final: 0.6459 (mtm) REVERT: A 877 LYS cc_start: 0.7491 (mmtp) cc_final: 0.7175 (mmtt) REVERT: A 898 ASP cc_start: 0.6635 (m-30) cc_final: 0.6405 (m-30) REVERT: A 925 LYS cc_start: 0.7797 (mptt) cc_final: 0.7589 (tppt) REVERT: A 1002 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7611 (mmp80) REVERT: B 321 ARG cc_start: 0.6831 (mmt180) cc_final: 0.6377 (mmt-90) REVERT: B 445 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: B 524 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7117 (tm-30) REVERT: B 607 LYS cc_start: 0.7168 (mtpt) cc_final: 0.6914 (mtpp) REVERT: B 635 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7702 (mm-30) REVERT: B 671 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8657 (tp) REVERT: B 685 ARG cc_start: 0.6004 (mtp180) cc_final: 0.5321 (tmt170) REVERT: B 694 ASN cc_start: 0.7531 (m-40) cc_final: 0.7003 (m-40) REVERT: B 719 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.7564 (mpt180) REVERT: B 877 LYS cc_start: 0.7468 (mmtp) cc_final: 0.7164 (mmtt) REVERT: B 898 ASP cc_start: 0.6678 (m-30) cc_final: 0.6459 (m-30) REVERT: B 909 LYS cc_start: 0.7196 (tttt) cc_final: 0.6897 (ttmm) REVERT: B 995 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7879 (tp30) outliers start: 30 outliers final: 12 residues processed: 161 average time/residue: 0.6527 time to fit residues: 114.1270 Evaluate side-chains 152 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 995 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 147 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 118 optimal weight: 0.4980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 900 ASN B 165 GLN B 286 GLN B 359 ASN B 701 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104251 restraints weight = 16231.332| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.15 r_work: 0.2946 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14382 Z= 0.087 Angle : 0.397 3.555 19560 Z= 0.211 Chirality : 0.038 0.138 2216 Planarity : 0.003 0.032 2430 Dihedral : 7.593 79.944 2056 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.94 % Allowed : 13.92 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1754 helix: 1.43 (0.18), residues: 986 sheet: 0.95 (0.45), residues: 146 loop : -1.60 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.008 0.001 TYR B 769 PHE 0.009 0.001 PHE B 380 TRP 0.009 0.001 TRP B 587 HIS 0.002 0.001 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (14376) covalent geometry : angle 0.39416 / 0.21 (19546) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 1.77463 / 0.86 ( 8) hydrogen bonds : bond 0.04795 / 3.16 ( 651) hydrogen bonds : angle 3.52171 / 2.61 ( 1890) link_NAG-ASN : bond 0.00138 / 0.07 ( 2) link_NAG-ASN : angle 1.69779 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.471 Fit side-chains REVERT: A 321 ARG cc_start: 0.6869 (mmt180) cc_final: 0.6535 (mmt-90) REVERT: A 407 ASP cc_start: 0.8010 (t70) cc_final: 0.6921 (t0) REVERT: A 635 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7805 (mm-30) REVERT: A 671 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 685 ARG cc_start: 0.5881 (mtp180) cc_final: 0.5344 (tmt170) REVERT: A 694 ASN cc_start: 0.7535 (m-40) cc_final: 0.7037 (m-40) REVERT: A 715 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 719 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7419 (mpt180) REVERT: A 872 MET cc_start: 0.6849 (mtp) cc_final: 0.6443 (mtm) REVERT: A 877 LYS cc_start: 0.7467 (mmtp) cc_final: 0.7147 (mmtt) REVERT: A 898 ASP cc_start: 0.6671 (m-30) cc_final: 0.6449 (m-30) REVERT: A 925 LYS cc_start: 0.7781 (mptt) cc_final: 0.7574 (tppt) REVERT: A 1002 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7608 (mmp80) REVERT: B 321 ARG cc_start: 0.6813 (mmt180) cc_final: 0.6317 (mmt-90) REVERT: B 445 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: B 524 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7112 (tm-30) REVERT: B 607 LYS cc_start: 0.7068 (mtpt) cc_final: 0.6829 (mtpp) REVERT: B 635 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7710 (mm-30) REVERT: B 671 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8640 (tp) REVERT: B 685 ARG cc_start: 0.5880 (mtp180) cc_final: 0.5284 (tmt170) REVERT: B 694 ASN cc_start: 0.7494 (m-40) cc_final: 0.6966 (m-40) REVERT: B 719 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7565 (mpt180) REVERT: B 877 LYS cc_start: 0.7453 (mmtp) cc_final: 0.7133 (mmtt) REVERT: B 898 ASP cc_start: 0.6746 (m-30) cc_final: 0.6537 (m-30) REVERT: B 909 LYS cc_start: 0.7153 (tttt) cc_final: 0.6843 (ttmm) REVERT: B 995 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7788 (tp30) outliers start: 29 outliers final: 17 residues processed: 152 average time/residue: 0.6555 time to fit residues: 107.8685 Evaluate side-chains 156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 988 SER Chi-restraints excluded: chain B residue 995 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 61 optimal weight: 0.0980 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 0.0470 chunk 32 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 900 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111502 restraints weight = 15984.922| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.04 r_work: 0.3060 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.034 14382 Z= 0.070 Angle : 0.365 3.477 19560 Z= 0.196 Chirality : 0.037 0.134 2216 Planarity : 0.003 0.032 2430 Dihedral : 7.290 77.726 2056 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.41 % Allowed : 14.73 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1754 helix: 1.79 (0.18), residues: 980 sheet: 1.12 (0.46), residues: 146 loop : -1.52 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.005 0.001 TYR A 966 PHE 0.007 0.001 PHE B 380 TRP 0.008 0.001 TRP A 587 HIS 0.001 0.000 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00146 / 0.07 (14376) covalent geometry : angle 0.36327 / 0.20 (19546) SS BOND : bond 0.00047 / 0.02 ( 4) SS BOND : angle 1.07839 / 0.52 ( 8) hydrogen bonds : bond 0.03891 / 2.56 ( 651) hydrogen bonds : angle 3.37800 / 2.50 ( 1890) link_NAG-ASN : bond 0.00084 / 0.04 ( 2) link_NAG-ASN : angle 1.76709 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.6918 (mmt180) cc_final: 0.6580 (mmt-90) REVERT: A 407 ASP cc_start: 0.8077 (t70) cc_final: 0.6941 (t0) REVERT: A 445 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 584 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5729 (mp) REVERT: A 635 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8237 (mm-30) REVERT: A 685 ARG cc_start: 0.5833 (mtp180) cc_final: 0.5366 (tmt170) REVERT: A 694 ASN cc_start: 0.7591 (m-40) cc_final: 0.7111 (m-40) REVERT: A 715 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 719 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7420 (mpt180) REVERT: A 872 MET cc_start: 0.6940 (mtp) cc_final: 0.6537 (mtm) REVERT: A 877 LYS cc_start: 0.7549 (mmtp) cc_final: 0.7241 (mmtt) REVERT: A 898 ASP cc_start: 0.6624 (m-30) cc_final: 0.6420 (m-30) REVERT: A 925 LYS cc_start: 0.7877 (mptt) cc_final: 0.7671 (tppt) REVERT: A 1002 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7624 (mmp80) REVERT: B 321 ARG cc_start: 0.6902 (mmt180) cc_final: 0.6396 (mmt-90) REVERT: B 445 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: B 524 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7066 (tm-30) REVERT: B 607 LYS cc_start: 0.7044 (mtpt) cc_final: 0.6812 (mtpp) REVERT: B 635 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7797 (mm-30) REVERT: B 671 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 685 ARG cc_start: 0.5940 (mtp180) cc_final: 0.5362 (tmt170) REVERT: B 694 ASN cc_start: 0.7569 (m-40) cc_final: 0.7068 (m-40) REVERT: B 877 LYS cc_start: 0.7575 (mmtp) cc_final: 0.7286 (mmtt) REVERT: B 909 LYS cc_start: 0.7291 (tttt) cc_final: 0.6990 (ttmm) REVERT: B 981 ARG cc_start: 0.8142 (ttt180) cc_final: 0.7929 (ttt180) REVERT: B 995 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7862 (tp30) outliers start: 21 outliers final: 10 residues processed: 151 average time/residue: 0.6652 time to fit residues: 108.8270 Evaluate side-chains 149 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 995 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 900 ASN B 165 GLN B 701 ASN B 762 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097513 restraints weight = 16033.338| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.12 r_work: 0.2937 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14382 Z= 0.106 Angle : 0.422 3.728 19560 Z= 0.223 Chirality : 0.039 0.141 2216 Planarity : 0.003 0.033 2430 Dihedral : 7.675 86.229 2056 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 14.86 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1754 helix: 1.67 (0.18), residues: 986 sheet: 0.93 (0.45), residues: 146 loop : -1.53 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 667 TYR 0.009 0.001 TYR B 769 PHE 0.012 0.001 PHE B 325 TRP 0.007 0.001 TRP B 699 HIS 0.002 0.001 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14376) covalent geometry : angle 0.42099 / 0.22 (19546) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 1.00083 / 0.48 ( 8) hydrogen bonds : bond 0.05416 / 3.57 ( 651) hydrogen bonds : angle 3.54537 / 2.62 ( 1890) link_NAG-ASN : bond 0.00261 / 0.13 ( 2) link_NAG-ASN : angle 1.54510 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.6861 (mmt180) cc_final: 0.6496 (mmt-90) REVERT: A 407 ASP cc_start: 0.7971 (t70) cc_final: 0.6877 (t0) REVERT: A 445 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: A 635 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7719 (mm-30) REVERT: A 685 ARG cc_start: 0.5815 (mtp180) cc_final: 0.5317 (tmt170) REVERT: A 694 ASN cc_start: 0.7488 (m-40) cc_final: 0.6992 (m-40) REVERT: A 715 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 719 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7377 (mpt180) REVERT: A 872 MET cc_start: 0.6891 (mtp) cc_final: 0.6459 (mtm) REVERT: A 877 LYS cc_start: 0.7382 (mmtp) cc_final: 0.7092 (mmtt) REVERT: A 898 ASP cc_start: 0.6600 (m-30) cc_final: 0.6395 (m-30) REVERT: A 925 LYS cc_start: 0.7719 (mptt) cc_final: 0.7516 (tppt) REVERT: A 1002 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7637 (mmp80) REVERT: B 321 ARG cc_start: 0.6812 (mmt180) cc_final: 0.6262 (mmt-90) REVERT: B 445 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: B 524 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7007 (tm-30) REVERT: B 583 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7012 (mp) REVERT: B 607 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6815 (mtpp) REVERT: B 635 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7711 (mm-30) REVERT: B 671 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 685 ARG cc_start: 0.5820 (mtp180) cc_final: 0.5256 (tmt170) REVERT: B 694 ASN cc_start: 0.7506 (m-40) cc_final: 0.6977 (m-40) REVERT: B 877 LYS cc_start: 0.7432 (mmtp) cc_final: 0.7155 (mmtt) REVERT: B 909 LYS cc_start: 0.7084 (tttt) cc_final: 0.6781 (ttmm) REVERT: B 1002 ARG cc_start: 0.7718 (mmt90) cc_final: 0.7291 (mpp80) outliers start: 29 outliers final: 20 residues processed: 156 average time/residue: 0.6699 time to fit residues: 113.4752 Evaluate side-chains 161 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 988 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 900 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN B 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.096862 restraints weight = 16005.462| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.12 r_work: 0.2884 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14382 Z= 0.110 Angle : 0.424 3.791 19560 Z= 0.226 Chirality : 0.039 0.144 2216 Planarity : 0.003 0.032 2430 Dihedral : 7.799 88.885 2056 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.07 % Allowed : 15.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1754 helix: 1.68 (0.18), residues: 978 sheet: 0.77 (0.44), residues: 146 loop : -1.50 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 775 TYR 0.010 0.001 TYR B 769 PHE 0.011 0.001 PHE B 380 TRP 0.008 0.001 TRP B 699 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14376) covalent geometry : angle 0.42336 / 0.23 (19546) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.92758 / 0.45 ( 8) hydrogen bonds : bond 0.05550 / 3.66 ( 651) hydrogen bonds : angle 3.60020 / 2.66 ( 1890) link_NAG-ASN : bond 0.00210 / 0.11 ( 2) link_NAG-ASN : angle 1.55764 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.6923 (mmt180) cc_final: 0.6567 (mmt-90) REVERT: A 407 ASP cc_start: 0.7991 (t70) cc_final: 0.6874 (t0) REVERT: A 445 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: A 635 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 671 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 685 ARG cc_start: 0.5785 (mtp180) cc_final: 0.5298 (tmt170) REVERT: A 686 MET cc_start: 0.4627 (mtp) cc_final: 0.4173 (mtt) REVERT: A 694 ASN cc_start: 0.7463 (m-40) cc_final: 0.6969 (m-40) REVERT: A 715 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 719 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7282 (mpt180) REVERT: A 872 MET cc_start: 0.6872 (mtp) cc_final: 0.6434 (mtm) REVERT: A 877 LYS cc_start: 0.7359 (mmtp) cc_final: 0.7061 (mmtt) REVERT: A 925 LYS cc_start: 0.7745 (mptt) cc_final: 0.7541 (tppt) REVERT: A 1002 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7654 (mmp80) REVERT: B 321 ARG cc_start: 0.6861 (mmt180) cc_final: 0.6306 (mmt-90) REVERT: B 445 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: B 524 GLU cc_start: 0.7896 (mt-10) cc_final: 0.6993 (tm-30) REVERT: B 607 LYS cc_start: 0.7013 (mtpt) cc_final: 0.6788 (mtpp) REVERT: B 635 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7655 (mm-30) REVERT: B 671 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8619 (tp) REVERT: B 685 ARG cc_start: 0.5793 (mtp180) cc_final: 0.5224 (tmt170) REVERT: B 686 MET cc_start: 0.4485 (mtp) cc_final: 0.4189 (mtt) REVERT: B 694 ASN cc_start: 0.7405 (m-40) cc_final: 0.6871 (m-40) REVERT: B 715 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 877 LYS cc_start: 0.7429 (mmtp) cc_final: 0.7144 (mmtt) REVERT: B 909 LYS cc_start: 0.7089 (tttt) cc_final: 0.6791 (ttmm) REVERT: B 1002 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7338 (mpp80) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 0.6735 time to fit residues: 115.5396 Evaluate side-chains 162 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 988 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 0.0470 chunk 133 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 900 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097320 restraints weight = 16186.775| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.11 r_work: 0.2957 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14382 Z= 0.083 Angle : 0.390 3.653 19560 Z= 0.209 Chirality : 0.038 0.138 2216 Planarity : 0.003 0.032 2430 Dihedral : 7.576 86.966 2056 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.87 % Allowed : 15.39 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1754 helix: 1.85 (0.18), residues: 982 sheet: 0.98 (0.46), residues: 142 loop : -1.43 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 703 TYR 0.007 0.001 TYR B 769 PHE 0.016 0.001 PHE B 325 TRP 0.013 0.001 TRP B 699 HIS 0.002 0.000 HIS B 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.08 (14376) covalent geometry : angle 0.38840 / 0.21 (19546) SS BOND : bond 0.00054 / 0.03 ( 4) SS BOND : angle 0.77713 / 0.38 ( 8) hydrogen bonds : bond 0.04708 / 3.10 ( 651) hydrogen bonds : angle 3.49779 / 2.59 ( 1890) link_NAG-ASN : bond 0.00112 / 0.06 ( 2) link_NAG-ASN : angle 1.63558 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.6869 (mmt180) cc_final: 0.6521 (mmt-90) REVERT: A 407 ASP cc_start: 0.8001 (t70) cc_final: 0.6926 (t0) REVERT: A 445 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: A 635 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7707 (mm-30) REVERT: A 671 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 685 ARG cc_start: 0.5795 (mtp180) cc_final: 0.5315 (tmt170) REVERT: A 686 MET cc_start: 0.4619 (mtp) cc_final: 0.4197 (mtt) REVERT: A 694 ASN cc_start: 0.7448 (m-40) cc_final: 0.6941 (m-40) REVERT: A 715 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 719 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7273 (mpt180) REVERT: A 872 MET cc_start: 0.6858 (mtp) cc_final: 0.6432 (mtm) REVERT: A 877 LYS cc_start: 0.7364 (mmtp) cc_final: 0.7065 (mmtt) REVERT: A 925 LYS cc_start: 0.7731 (mptt) cc_final: 0.7527 (tppt) REVERT: A 1002 ARG cc_start: 0.8234 (mmt180) cc_final: 0.7616 (mmp80) REVERT: B 321 ARG cc_start: 0.6841 (mmt180) cc_final: 0.6288 (mmt-90) REVERT: B 445 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 524 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7009 (tm-30) REVERT: B 607 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6730 (mtpp) REVERT: B 635 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7651 (mm-30) REVERT: B 671 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8607 (tp) REVERT: B 685 ARG cc_start: 0.5760 (mtp180) cc_final: 0.5262 (tmt170) REVERT: B 686 MET cc_start: 0.4562 (mtp) cc_final: 0.4275 (mtt) REVERT: B 694 ASN cc_start: 0.7414 (m-40) cc_final: 0.6868 (m-40) REVERT: B 715 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 877 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7147 (mmtt) REVERT: B 909 LYS cc_start: 0.7105 (tttt) cc_final: 0.6806 (ttmm) REVERT: B 995 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: B 1002 ARG cc_start: 0.7668 (mmt90) cc_final: 0.7255 (mpp80) outliers start: 28 outliers final: 21 residues processed: 150 average time/residue: 0.7076 time to fit residues: 115.1190 Evaluate side-chains 159 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 988 SER Chi-restraints excluded: chain B residue 995 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 94 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 chunk 30 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 900 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095773 restraints weight = 16132.827| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.14 r_work: 0.2906 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14382 Z= 0.124 Angle : 0.450 4.000 19560 Z= 0.237 Chirality : 0.039 0.144 2216 Planarity : 0.004 0.033 2430 Dihedral : 7.887 87.349 2056 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.74 % Allowed : 15.80 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1754 helix: 1.68 (0.18), residues: 978 sheet: 0.84 (0.45), residues: 142 loop : -1.46 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 775 TYR 0.012 0.001 TYR B 769 PHE 0.012 0.001 PHE B 380 TRP 0.009 0.001 TRP B 699 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (14376) covalent geometry : angle 0.44878 / 0.24 (19546) SS BOND : bond 0.00088 / 0.04 ( 4) SS BOND : angle 0.87607 / 0.42 ( 8) hydrogen bonds : bond 0.05972 / 3.94 ( 651) hydrogen bonds : angle 3.64192 / 2.69 ( 1890) link_NAG-ASN : bond 0.00259 / 0.13 ( 2) link_NAG-ASN : angle 1.49307 / 0.80 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3508 Ramachandran restraints generated. 1754 Oldfield, 0 Emsley, 1754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.6979 (mmt180) cc_final: 0.6617 (mmt-90) REVERT: A 407 ASP cc_start: 0.8013 (t70) cc_final: 0.6894 (t0) REVERT: A 445 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: A 635 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7714 (mm-30) REVERT: A 671 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8644 (tp) REVERT: A 685 ARG cc_start: 0.5810 (mtp180) cc_final: 0.5323 (tmt170) REVERT: A 686 MET cc_start: 0.4626 (mtp) cc_final: 0.4218 (mtt) REVERT: A 694 ASN cc_start: 0.7507 (m-40) cc_final: 0.7007 (m-40) REVERT: A 715 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 719 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7327 (mpt180) REVERT: A 872 MET cc_start: 0.6964 (mtp) cc_final: 0.6554 (mtm) REVERT: A 877 LYS cc_start: 0.7339 (mmtp) cc_final: 0.7042 (mmtt) REVERT: A 898 ASP cc_start: 0.6700 (m-30) cc_final: 0.6431 (m-30) REVERT: A 925 LYS cc_start: 0.7782 (mptt) cc_final: 0.7576 (tppt) REVERT: A 1002 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7668 (mmp80) REVERT: B 321 ARG cc_start: 0.6878 (mmt180) cc_final: 0.6316 (mmt-90) REVERT: B 445 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: B 524 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7006 (tm-30) REVERT: B 607 LYS cc_start: 0.7016 (mtpt) cc_final: 0.6779 (mtpp) REVERT: B 635 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7669 (mm-30) REVERT: B 671 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8636 (tp) REVERT: B 685 ARG cc_start: 0.5785 (mtp180) cc_final: 0.5251 (tmt170) REVERT: B 686 MET cc_start: 0.4513 (mtp) cc_final: 0.4248 (mtt) REVERT: B 694 ASN cc_start: 0.7518 (m-40) cc_final: 0.6975 (m-40) REVERT: B 715 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 877 LYS cc_start: 0.7390 (mmtp) cc_final: 0.7105 (mmtt) REVERT: B 909 LYS cc_start: 0.7118 (tttt) cc_final: 0.6817 (ttmm) REVERT: B 1002 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7386 (mpp80) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.6992 time to fit residues: 114.0943 Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 988 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 116 optimal weight: 30.0000 chunk 5 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 145 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 900 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095915 restraints weight = 16000.073| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.14 r_work: 0.2887 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14382 Z= 0.127 Angle : 0.727 59.198 19560 Z= 0.438 Chirality : 0.039 0.146 2216 Planarity : 0.004 0.033 2430 Dihedral : 7.898 87.308 2056 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 15.80 % Favored : 82.46 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1754 helix: 1.65 (0.18), residues: 978 sheet: 0.84 (0.45), residues: 142 loop : -1.46 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 243 TYR 0.012 0.001 TYR B 769 PHE 0.012 0.001 PHE B 380 TRP 0.009 0.001 TRP B 699 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14376) covalent geometry : angle 0.72612 / 0.44 (19546) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.84558 / 0.41 ( 8) hydrogen bonds : bond 0.05856 / 3.86 ( 651) hydrogen bonds : angle 3.65264 / 2.70 ( 1890) link_NAG-ASN : bond 0.00240 / 0.12 ( 2) link_NAG-ASN : angle 1.49716 / 0.80 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4959.68 seconds wall clock time: 85 minutes 5.60 seconds (5105.60 seconds total)