Starting phenix.real_space_refine on Thu Mar 5 05:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1p_0594/03_2026/6o1p_0594.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Restraints were copied for chains: B, C, D Time building chain proxies: 3.82, per 1000 atoms: 0.19 Number of scatterers: 19608 At special positions: 0 Unit cell: (132.375, 132.375, 124.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 807.0 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 59.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.711A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.619A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.954A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.711A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 443 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.513A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.928A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.740A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.711A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 443 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 removed outlier: 3.633A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.512A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.711A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 443 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.551A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 266 Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 266 Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 266 820 hydrogen bonds defined for protein. 2352 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: 2.13 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3484 1.32 - 1.45: 5405 1.45 - 1.57: 10947 1.57 - 1.70: 0 1.70 - 1.83: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" CA TRP B 286 " pdb=" C TRP B 286 " ideal model delta sigma weight residual 1.526 1.422 0.103 1.31e-02 5.83e+03 6.21e+01 bond pdb=" CA TRP D 286 " pdb=" C TRP D 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP A 286 " pdb=" C TRP A 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP C 286 " pdb=" C TRP C 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" N TRP A 286 " pdb=" CA TRP A 286 " ideal model delta sigma weight residual 1.458 1.380 0.078 1.00e-02 1.00e+04 6.12e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 26880 5.04 - 10.08: 303 10.08 - 15.11: 32 15.11 - 20.15: 13 20.15 - 25.19: 20 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N LEU B 612 " pdb=" CA LEU B 612 " pdb=" C LEU B 612 " ideal model delta sigma weight residual 111.04 136.05 -25.01 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU C 612 " pdb=" CA LEU C 612 " pdb=" C LEU C 612 " ideal model delta sigma weight residual 111.04 136.03 -24.99 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU A 612 " pdb=" CA LEU A 612 " pdb=" C LEU A 612 " ideal model delta sigma weight residual 111.04 136.02 -24.98 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 111.04 136.01 -24.97 1.55e+00 4.16e-01 2.59e+02 angle pdb=" N LEU C 354 " pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 108.99 85.57 23.42 1.57e+00 4.06e-01 2.23e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 11120 15.24 - 30.47: 652 30.47 - 45.71: 144 45.71 - 60.94: 8 60.94 - 76.18: 12 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" N TRP C 613 " pdb=" C TRP C 613 " pdb=" CA TRP C 613 " pdb=" CB TRP C 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP D 613 " pdb=" C TRP D 613 " pdb=" CA TRP D 613 " pdb=" CB TRP D 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP A 613 " pdb=" C TRP A 613 " pdb=" CA TRP A 613 " pdb=" CB TRP A 613 " ideal model delta harmonic sigma weight residual 122.80 92.86 29.94 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3036 0.199 - 0.397: 48 0.397 - 0.596: 4 0.596 - 0.795: 8 0.795 - 0.993: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA LEU C 612 " pdb=" N LEU C 612 " pdb=" C LEU C 612 " pdb=" CB LEU C 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA LEU B 612 " pdb=" N LEU B 612 " pdb=" C LEU B 612 " pdb=" CB LEU B 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA LEU A 612 " pdb=" N LEU A 612 " pdb=" C LEU A 612 " pdb=" CB LEU A 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER B 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER B 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP B 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 285 " -0.053 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER D 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER D 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP D 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER A 285 " 0.210 2.00e-02 2.50e+03 pdb=" O SER A 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP A 286 " -0.071 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 79 2.50 - 3.10: 13170 3.10 - 3.70: 30008 3.70 - 4.30: 44383 4.30 - 4.90: 71847 Nonbonded interactions: 159487 Sorted by model distance: nonbonded pdb=" O SER B 285 " pdb=" CD1 TRP B 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER D 285 " pdb=" CD1 TRP D 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER A 285 " pdb=" CD1 TRP A 286 " model vdw 1.900 3.260 nonbonded pdb=" O SER C 285 " pdb=" CD1 TRP C 286 " model vdw 1.900 3.260 nonbonded pdb=" N GLN A 230 " pdb=" OE1 GLN A 230 " model vdw 2.096 3.120 ... (remaining 159482 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.012 0.145 20064 Z= 0.551 Angle : 1.528 25.188 27248 Z= 0.875 Chirality : 0.087 0.993 3100 Planarity : 0.009 0.122 3460 Dihedral : 10.643 76.176 7312 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.79 % Rotamer: Outliers : 0.57 % Allowed : 1.32 % Favored : 98.11 % Cbeta Deviations : 1.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.75 (0.12), residues: 2440 helix: -3.98 (0.07), residues: 1428 sheet: -3.16 (0.62), residues: 64 loop : -3.31 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 470 TYR 0.045 0.004 TYR B 349 PHE 0.041 0.004 PHE C 508 TRP 0.075 0.006 TRP B 286 HIS 0.016 0.003 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.01228 (20064) covalent geometry : angle 1.52768 (27248) hydrogen bonds : bond 0.31347 ( 820) hydrogen bonds : angle 10.49110 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 607 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8463 (p) cc_final: 0.8108 (t) REVERT: A 301 LYS cc_start: 0.8184 (tptm) cc_final: 0.7788 (mmmt) REVERT: B 114 PRO cc_start: 0.8021 (Cg_endo) cc_final: 0.7523 (Cg_exo) REVERT: B 208 ASN cc_start: 0.5430 (t0) cc_final: 0.4744 (p0) REVERT: C 301 LYS cc_start: 0.8249 (tptm) cc_final: 0.7887 (mmmt) REVERT: C 554 MET cc_start: 0.8165 (tpt) cc_final: 0.7945 (tpt) REVERT: C 565 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 379 THR cc_start: 0.7523 (t) cc_final: 0.6894 (m) outliers start: 12 outliers final: 4 residues processed: 616 average time/residue: 0.6175 time to fit residues: 425.1499 Evaluate side-chains 358 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 353 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 621 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 51 GLN A 157 HIS A 238 HIS A 265 HIS A 446 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 51 GLN B 157 HIS B 158 ASN B 238 HIS B 446 ASN B 473 GLN B 519 ASN B 582 HIS C 238 HIS C 446 ASN C 473 GLN D 128 GLN D 157 HIS D 214 GLN D 238 HIS D 265 HIS D 310 GLN D 446 ASN D 582 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129780 restraints weight = 25509.068| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.94 r_work: 0.3336 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.141 Angle : 0.715 10.634 27248 Z= 0.365 Chirality : 0.043 0.167 3100 Planarity : 0.006 0.047 3460 Dihedral : 6.352 47.686 2682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.67 % Allowed : 13.68 % Favored : 81.65 % 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: -3.64 (0.15), residues: 2440 helix: -2.12 (0.11), residues: 1408 sheet: -2.24 (0.68), residues: 56 loop : -2.72 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 628 TYR 0.018 0.002 TYR B 559 PHE 0.016 0.002 PHE D 211 TRP 0.027 0.002 TRP C 613 HIS 0.006 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00312 (20064) covalent geometry : angle 0.71458 (27248) hydrogen bonds : bond 0.04397 ( 820) hydrogen bonds : angle 4.97013 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 443 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6832 (mp0) REVERT: A 39 LEU cc_start: 0.8834 (tp) cc_final: 0.8501 (mt) REVERT: A 126 MET cc_start: 0.7772 (mmm) cc_final: 0.7405 (mtm) REVERT: A 301 LYS cc_start: 0.8635 (tptm) cc_final: 0.8258 (tptp) REVERT: A 303 GLU cc_start: 0.8440 (mp0) cc_final: 0.7970 (mp0) REVERT: A 409 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8204 (mtp85) REVERT: A 442 MET cc_start: 0.8607 (mmt) cc_final: 0.7682 (mmt) REVERT: A 637 HIS cc_start: 0.7321 (m-70) cc_final: 0.7025 (m-70) REVERT: B 35 ARG cc_start: 0.7428 (mmt90) cc_final: 0.6706 (mmt-90) REVERT: B 49 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7973 (pp) REVERT: B 129 ASN cc_start: 0.7363 (t0) cc_final: 0.7040 (t0) REVERT: B 208 ASN cc_start: 0.6029 (t0) cc_final: 0.4728 (p0) REVERT: B 282 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: B 382 ASP cc_start: 0.8048 (m-30) cc_final: 0.7842 (m-30) REVERT: B 555 TYR cc_start: 0.8016 (t80) cc_final: 0.7766 (t80) REVERT: B 578 MET cc_start: 0.8133 (mtp) cc_final: 0.7922 (mtp) REVERT: B 603 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (ptm) REVERT: B 613 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.3789 (m-90) REVERT: C 286 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7883 (m100) REVERT: C 627 ASP cc_start: 0.8299 (t0) cc_final: 0.8055 (t0) REVERT: C 637 HIS cc_start: 0.7104 (m-70) cc_final: 0.6897 (m-70) REVERT: D 38 MET cc_start: 0.8550 (mtp) cc_final: 0.8225 (mtm) REVERT: D 97 LEU cc_start: 0.8655 (mm) cc_final: 0.8232 (mm) REVERT: D 425 PHE cc_start: 0.8467 (m-80) cc_final: 0.8245 (m-80) REVERT: D 596 GLN cc_start: 0.8555 (tt0) cc_final: 0.8351 (tt0) REVERT: D 603 MET cc_start: 0.8421 (tmm) cc_final: 0.8071 (tmm) REVERT: D 622 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: D 623 TYR cc_start: 0.7526 (m-80) cc_final: 0.7011 (m-80) outliers start: 99 outliers final: 26 residues processed: 497 average time/residue: 0.5696 time to fit residues: 319.5326 Evaluate side-chains 375 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 613 TRP Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 206 GLN A 518 ASN A 519 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 31 GLN B 128 GLN B 157 HIS B 519 ASN C 237 ASN C 257 GLN C 267 GLN D 51 GLN D 157 HIS D 158 ASN D 214 GLN D 265 HIS D 587 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.160108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125702 restraints weight = 25285.134| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.06 r_work: 0.3247 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20064 Z= 0.143 Angle : 0.663 12.703 27248 Z= 0.334 Chirality : 0.042 0.205 3100 Planarity : 0.005 0.042 3460 Dihedral : 5.663 58.129 2674 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.29 % Allowed : 17.78 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.16), residues: 2440 helix: -0.94 (0.13), residues: 1408 sheet: -2.21 (0.65), residues: 56 loop : -2.59 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 305 TYR 0.020 0.002 TYR B 559 PHE 0.014 0.001 PHE B 211 TRP 0.015 0.001 TRP C 613 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00338 (20064) covalent geometry : angle 0.66280 (27248) hydrogen bonds : bond 0.03828 ( 820) hydrogen bonds : angle 4.28800 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 395 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7109 (mp0) REVERT: A 80 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: A 176 GLU cc_start: 0.8575 (pm20) cc_final: 0.8352 (pm20) REVERT: A 442 MET cc_start: 0.8636 (mmt) cc_final: 0.7856 (mmt) REVERT: A 622 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 47 SER cc_start: 0.7590 (t) cc_final: 0.7385 (m) REVERT: B 139 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6891 (mtm-85) REVERT: B 274 THR cc_start: 0.8687 (p) cc_final: 0.8283 (p) REVERT: C 129 ASN cc_start: 0.8622 (t0) cc_final: 0.8351 (t0) REVERT: C 627 ASP cc_start: 0.8126 (t0) cc_final: 0.7906 (t0) REVERT: D 38 MET cc_start: 0.8456 (mtp) cc_final: 0.8153 (mtm) REVERT: D 80 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: D 97 LEU cc_start: 0.8737 (mm) cc_final: 0.8535 (mm) REVERT: D 491 MET cc_start: 0.8251 (ptt) cc_final: 0.7639 (mmt) REVERT: D 525 ASP cc_start: 0.7889 (m-30) cc_final: 0.7673 (m-30) REVERT: D 588 GLU cc_start: 0.8285 (tp30) cc_final: 0.7922 (mt-10) REVERT: D 603 MET cc_start: 0.8643 (tmm) cc_final: 0.8337 (tmm) REVERT: D 622 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: D 623 TYR cc_start: 0.7513 (m-80) cc_final: 0.6964 (m-80) outliers start: 91 outliers final: 33 residues processed: 444 average time/residue: 0.5531 time to fit residues: 278.0506 Evaluate side-chains 371 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 613 TRP Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 152 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS B 129 ASN B 157 HIS B 519 ASN C 237 ASN C 257 GLN C 310 GLN D 265 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122680 restraints weight = 25198.133| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.09 r_work: 0.3199 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20064 Z= 0.150 Angle : 0.644 10.878 27248 Z= 0.324 Chirality : 0.043 0.191 3100 Planarity : 0.004 0.044 3460 Dihedral : 5.330 24.599 2672 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.77 % Allowed : 19.76 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2440 helix: -0.40 (0.13), residues: 1408 sheet: -2.31 (0.60), residues: 56 loop : -2.37 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 610 TYR 0.023 0.002 TYR D 32 PHE 0.019 0.001 PHE C 553 TRP 0.013 0.001 TRP C 613 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00364 (20064) covalent geometry : angle 0.64399 (27248) hydrogen bonds : bond 0.03590 ( 820) hydrogen bonds : angle 4.07720 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 374 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASN cc_start: 0.7049 (t0) cc_final: 0.6826 (t0) REVERT: A 622 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: A 623 TYR cc_start: 0.6732 (m-80) cc_final: 0.6325 (m-80) REVERT: B 47 SER cc_start: 0.7705 (t) cc_final: 0.7492 (m) REVERT: B 286 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.7701 (m100) REVERT: C 627 ASP cc_start: 0.8201 (t0) cc_final: 0.7932 (t0) REVERT: D 254 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.9024 (m) REVERT: D 286 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.7270 (m100) REVERT: D 341 ILE cc_start: 0.8734 (pt) cc_final: 0.8530 (mt) REVERT: D 491 MET cc_start: 0.8148 (ptt) cc_final: 0.7741 (mmt) outliers start: 80 outliers final: 34 residues processed: 421 average time/residue: 0.5327 time to fit residues: 254.7573 Evaluate side-chains 367 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 156 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 234 optimal weight: 0.2980 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 518 ASN B 129 ASN B 157 HIS B 310 GLN B 519 ASN C 51 GLN C 257 GLN C 310 GLN D 265 HIS D 518 ASN D 519 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125372 restraints weight = 25172.740| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.92 r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20064 Z= 0.118 Angle : 0.618 9.528 27248 Z= 0.310 Chirality : 0.042 0.192 3100 Planarity : 0.004 0.064 3460 Dihedral : 5.103 22.974 2672 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.54 % Allowed : 21.70 % Favored : 74.76 % 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: -1.42 (0.17), residues: 2440 helix: 0.00 (0.14), residues: 1400 sheet: -2.24 (0.57), residues: 56 loop : -2.26 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 45 TYR 0.023 0.002 TYR D 32 PHE 0.020 0.001 PHE C 553 TRP 0.011 0.001 TRP A 286 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00274 (20064) covalent geometry : angle 0.61782 (27248) hydrogen bonds : bond 0.03316 ( 820) hydrogen bonds : angle 3.87876 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 357 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 623 TYR cc_start: 0.6531 (m-80) cc_final: 0.6094 (m-80) REVERT: B 47 SER cc_start: 0.7659 (t) cc_final: 0.7427 (m) REVERT: B 238 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7369 (m90) REVERT: B 274 THR cc_start: 0.8701 (p) cc_final: 0.8498 (p) REVERT: B 332 LEU cc_start: 0.8360 (tt) cc_final: 0.8143 (tp) REVERT: B 447 MET cc_start: 0.8135 (mmm) cc_final: 0.7891 (tpp) REVERT: B 608 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8533 (mtp) REVERT: B 610 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7564 (mmp-170) REVERT: C 38 MET cc_start: 0.7662 (mtp) cc_final: 0.7425 (mtm) REVERT: C 39 LEU cc_start: 0.8877 (mt) cc_final: 0.8674 (mt) REVERT: C 80 GLU cc_start: 0.8405 (pm20) cc_final: 0.7832 (pp20) REVERT: C 382 ASP cc_start: 0.7457 (m-30) cc_final: 0.7064 (m-30) REVERT: C 627 ASP cc_start: 0.8110 (t0) cc_final: 0.7846 (t0) REVERT: D 211 PHE cc_start: 0.8023 (m-80) cc_final: 0.7648 (m-10) REVERT: D 491 MET cc_start: 0.8013 (ptt) cc_final: 0.7710 (mmt) REVERT: D 581 THR cc_start: 0.9276 (t) cc_final: 0.9058 (p) REVERT: D 622 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: D 623 TYR cc_start: 0.7445 (m-80) cc_final: 0.6978 (m-80) outliers start: 75 outliers final: 27 residues processed: 400 average time/residue: 0.5179 time to fit residues: 235.9403 Evaluate side-chains 363 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 332 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 519 ASN B 129 ASN B 157 HIS C 519 ASN D 31 GLN D 518 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123383 restraints weight = 25024.869| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.99 r_work: 0.3208 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20064 Z= 0.134 Angle : 0.623 10.501 27248 Z= 0.312 Chirality : 0.042 0.194 3100 Planarity : 0.004 0.050 3460 Dihedral : 5.007 22.795 2672 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.01 % Allowed : 20.75 % Favored : 75.24 % 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: -1.17 (0.17), residues: 2440 helix: 0.18 (0.14), residues: 1404 sheet: -2.15 (0.55), residues: 56 loop : -2.11 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 45 TYR 0.024 0.002 TYR D 555 PHE 0.022 0.001 PHE C 553 TRP 0.012 0.001 TRP A 29 HIS 0.007 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00324 (20064) covalent geometry : angle 0.62277 (27248) hydrogen bonds : bond 0.03332 ( 820) hydrogen bonds : angle 3.87840 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 361 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6444 (m100) REVERT: A 294 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: A 588 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: B 47 SER cc_start: 0.7723 (t) cc_final: 0.7427 (m) REVERT: B 238 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7445 (m90) REVERT: B 274 THR cc_start: 0.8717 (p) cc_final: 0.8427 (t) REVERT: B 603 MET cc_start: 0.8619 (tmm) cc_final: 0.8316 (ttt) REVERT: C 38 MET cc_start: 0.7773 (mtp) cc_final: 0.7514 (mtm) REVERT: C 80 GLU cc_start: 0.8438 (pm20) cc_final: 0.7789 (pp20) REVERT: C 627 ASP cc_start: 0.8181 (t0) cc_final: 0.7930 (t0) REVERT: D 47 SER cc_start: 0.7884 (t) cc_final: 0.7603 (m) REVERT: D 211 PHE cc_start: 0.8124 (m-80) cc_final: 0.7770 (m-10) REVERT: D 286 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.7083 (m100) REVERT: D 294 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: D 491 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7747 (mmt) REVERT: D 581 THR cc_start: 0.9266 (t) cc_final: 0.9060 (p) REVERT: D 622 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: D 623 TYR cc_start: 0.7429 (m-80) cc_final: 0.6989 (m-80) outliers start: 85 outliers final: 36 residues processed: 409 average time/residue: 0.5124 time to fit residues: 238.3889 Evaluate side-chains 373 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 24 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 157 HIS A 158 ASN A 208 ASN A 310 GLN A 518 ASN A 519 ASN B 129 ASN B 518 ASN B 519 ASN D 518 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124040 restraints weight = 25312.842| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.07 r_work: 0.3216 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.120 Angle : 0.619 10.774 27248 Z= 0.309 Chirality : 0.042 0.159 3100 Planarity : 0.004 0.077 3460 Dihedral : 4.939 21.927 2672 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.96 % Allowed : 21.23 % Favored : 74.81 % 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: -0.96 (0.17), residues: 2440 helix: 0.33 (0.14), residues: 1404 sheet: -2.00 (0.56), residues: 76 loop : -1.97 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 146 TYR 0.024 0.002 TYR D 32 PHE 0.023 0.001 PHE C 553 TRP 0.012 0.001 TRP B 29 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00284 (20064) covalent geometry : angle 0.61935 (27248) hydrogen bonds : bond 0.03267 ( 820) hydrogen bonds : angle 3.83582 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 348 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 GLN cc_start: 0.8086 (tp40) cc_final: 0.7844 (mm110) REVERT: A 286 TRP cc_start: 0.7284 (OUTLIER) cc_final: 0.6386 (m100) REVERT: A 294 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: A 442 MET cc_start: 0.8633 (mtp) cc_final: 0.7635 (mmt) REVERT: A 588 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: B 47 SER cc_start: 0.7776 (t) cc_final: 0.7463 (m) REVERT: B 238 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7481 (m90) REVERT: B 303 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8140 (mp0) REVERT: C 38 MET cc_start: 0.7869 (mtp) cc_final: 0.7648 (mtm) REVERT: C 39 LEU cc_start: 0.8869 (mt) cc_final: 0.8636 (mt) REVERT: C 80 GLU cc_start: 0.8435 (pm20) cc_final: 0.7786 (pp20) REVERT: C 627 ASP cc_start: 0.8247 (t0) cc_final: 0.7986 (t0) REVERT: D 47 SER cc_start: 0.8070 (t) cc_final: 0.7859 (m) REVERT: D 211 PHE cc_start: 0.8085 (m-80) cc_final: 0.7660 (m-10) REVERT: D 286 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.7024 (m100) REVERT: D 294 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: D 491 MET cc_start: 0.7975 (ptt) cc_final: 0.7674 (mmp) REVERT: D 580 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8441 (t70) REVERT: D 622 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: D 623 TYR cc_start: 0.7289 (m-80) cc_final: 0.6861 (m-80) outliers start: 84 outliers final: 35 residues processed: 399 average time/residue: 0.5287 time to fit residues: 239.7702 Evaluate side-chains 364 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 155 optimal weight: 0.2980 chunk 210 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 518 ASN A 519 ASN B 129 ASN B 519 ASN C 310 GLN C 519 ASN D 518 ASN D 519 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121758 restraints weight = 25106.784| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.16 r_work: 0.3172 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20064 Z= 0.150 Angle : 0.643 10.175 27248 Z= 0.321 Chirality : 0.043 0.170 3100 Planarity : 0.004 0.063 3460 Dihedral : 4.979 22.618 2672 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.35 % Allowed : 22.59 % Favored : 74.06 % 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: -0.93 (0.17), residues: 2440 helix: 0.38 (0.14), residues: 1400 sheet: -1.68 (0.56), residues: 56 loop : -2.03 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 146 TYR 0.035 0.002 TYR A 621 PHE 0.023 0.001 PHE C 553 TRP 0.012 0.001 TRP B 29 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00365 (20064) covalent geometry : angle 0.64296 (27248) hydrogen bonds : bond 0.03393 ( 820) hydrogen bonds : angle 3.94166 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 345 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.7315 (OUTLIER) cc_final: 0.6430 (m100) REVERT: A 294 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 442 MET cc_start: 0.8625 (mtp) cc_final: 0.7553 (mmt) REVERT: A 490 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8086 (tp) REVERT: A 588 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 238 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7624 (m90) REVERT: B 274 THR cc_start: 0.8797 (p) cc_final: 0.8497 (t) REVERT: B 303 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8223 (mp0) REVERT: C 38 MET cc_start: 0.7903 (mtp) cc_final: 0.7680 (mtm) REVERT: C 47 SER cc_start: 0.7838 (t) cc_final: 0.7539 (m) REVERT: C 80 GLU cc_start: 0.8497 (pm20) cc_final: 0.7861 (pp20) REVERT: C 627 ASP cc_start: 0.8287 (t0) cc_final: 0.8039 (t0) REVERT: D 47 SER cc_start: 0.8133 (t) cc_final: 0.7929 (m) REVERT: D 211 PHE cc_start: 0.8079 (m-80) cc_final: 0.7732 (m-10) REVERT: D 286 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.6988 (m100) REVERT: D 294 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: D 322 LYS cc_start: 0.8625 (mptt) cc_final: 0.8421 (mmtm) REVERT: D 491 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7734 (mmp) REVERT: D 622 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: D 623 TYR cc_start: 0.7274 (m-80) cc_final: 0.6923 (m-80) outliers start: 71 outliers final: 41 residues processed: 389 average time/residue: 0.5365 time to fit residues: 236.4184 Evaluate side-chains 374 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 518 ASN A 519 ASN B 157 HIS C 257 GLN C 310 GLN D 518 ASN D 519 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122430 restraints weight = 24754.030| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.16 r_work: 0.3174 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20064 Z= 0.133 Angle : 0.651 17.988 27248 Z= 0.324 Chirality : 0.043 0.414 3100 Planarity : 0.004 0.064 3460 Dihedral : 4.948 22.117 2672 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.02 % Allowed : 23.40 % Favored : 73.58 % 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: -0.84 (0.17), residues: 2440 helix: 0.45 (0.14), residues: 1400 sheet: -1.50 (0.57), residues: 56 loop : -1.99 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 45 TYR 0.032 0.002 TYR A 32 PHE 0.023 0.001 PHE A 553 TRP 0.009 0.001 TRP C 286 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00319 (20064) covalent geometry : angle 0.65148 (27248) hydrogen bonds : bond 0.03303 ( 820) hydrogen bonds : angle 3.92737 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8215 (tp30) cc_final: 0.7927 (tp30) REVERT: A 286 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6460 (m100) REVERT: A 294 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 442 MET cc_start: 0.8621 (mtp) cc_final: 0.7573 (mmt) REVERT: A 490 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8093 (tp) REVERT: A 588 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: B 39 LEU cc_start: 0.8684 (mm) cc_final: 0.8484 (mp) REVERT: B 183 ILE cc_start: 0.8722 (mm) cc_final: 0.8512 (mm) REVERT: B 238 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7632 (m90) REVERT: B 274 THR cc_start: 0.8844 (p) cc_final: 0.8562 (t) REVERT: B 303 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8295 (mp0) REVERT: C 38 MET cc_start: 0.7853 (mtp) cc_final: 0.7645 (mtm) REVERT: C 39 LEU cc_start: 0.8913 (mt) cc_final: 0.8705 (mt) REVERT: C 47 SER cc_start: 0.7882 (t) cc_final: 0.7587 (m) REVERT: C 80 GLU cc_start: 0.8514 (pm20) cc_final: 0.7849 (pp20) REVERT: C 257 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7857 (mp-120) REVERT: C 627 ASP cc_start: 0.8317 (t0) cc_final: 0.8066 (t0) REVERT: D 32 TYR cc_start: 0.7475 (t80) cc_final: 0.7218 (t80) REVERT: D 113 GLU cc_start: 0.7608 (mp0) cc_final: 0.7286 (pm20) REVERT: D 211 PHE cc_start: 0.8121 (m-80) cc_final: 0.7800 (m-10) REVERT: D 286 TRP cc_start: 0.7343 (OUTLIER) cc_final: 0.6918 (m100) REVERT: D 294 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7566 (tp30) REVERT: D 491 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7657 (mmp) REVERT: D 622 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: D 623 TYR cc_start: 0.7199 (m-80) cc_final: 0.6874 (m-80) outliers start: 64 outliers final: 30 residues processed: 378 average time/residue: 0.5448 time to fit residues: 232.8559 Evaluate side-chains 366 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 64 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 152 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 518 ASN A 519 ASN B 157 HIS B 257 GLN B 310 GLN C 257 GLN D 518 ASN D 519 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124372 restraints weight = 25171.891| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.18 r_work: 0.3190 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20064 Z= 0.127 Angle : 0.659 18.052 27248 Z= 0.326 Chirality : 0.043 0.409 3100 Planarity : 0.004 0.060 3460 Dihedral : 4.903 21.604 2672 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.36 % Allowed : 24.58 % Favored : 73.07 % 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: -0.75 (0.17), residues: 2440 helix: 0.51 (0.14), residues: 1400 sheet: -1.37 (0.57), residues: 56 loop : -1.95 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 45 TYR 0.025 0.002 TYR D 555 PHE 0.024 0.001 PHE A 553 TRP 0.008 0.001 TRP D 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00299 (20064) covalent geometry : angle 0.65867 (27248) hydrogen bonds : bond 0.03244 ( 820) hydrogen bonds : angle 3.88968 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 339 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.8271 (tp30) cc_final: 0.7917 (tp30) REVERT: A 286 TRP cc_start: 0.7137 (OUTLIER) cc_final: 0.6290 (m100) REVERT: A 294 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 442 MET cc_start: 0.8640 (mtp) cc_final: 0.7609 (mmt) REVERT: A 490 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 588 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: B 183 ILE cc_start: 0.8744 (mm) cc_final: 0.8530 (mm) REVERT: B 238 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7689 (m90) REVERT: B 274 THR cc_start: 0.8854 (p) cc_final: 0.8599 (t) REVERT: B 303 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8298 (mp0) REVERT: C 39 LEU cc_start: 0.8880 (mt) cc_final: 0.8660 (mt) REVERT: C 47 SER cc_start: 0.7786 (t) cc_final: 0.7508 (m) REVERT: C 80 GLU cc_start: 0.8491 (pm20) cc_final: 0.7875 (pp20) REVERT: C 176 GLU cc_start: 0.8390 (pm20) cc_final: 0.8171 (pm20) REVERT: C 257 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7703 (mp-120) REVERT: C 627 ASP cc_start: 0.8281 (t0) cc_final: 0.8011 (t0) REVERT: D 32 TYR cc_start: 0.7424 (t80) cc_final: 0.7209 (t80) REVERT: D 113 GLU cc_start: 0.7615 (mp0) cc_final: 0.7387 (pm20) REVERT: D 211 PHE cc_start: 0.8127 (m-80) cc_final: 0.7777 (m-10) REVERT: D 282 GLU cc_start: 0.8813 (mp0) cc_final: 0.8497 (mm-30) REVERT: D 286 TRP cc_start: 0.7243 (OUTLIER) cc_final: 0.6829 (m100) REVERT: D 294 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: D 491 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7542 (mmp) REVERT: D 622 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: D 623 TYR cc_start: 0.7142 (m-80) cc_final: 0.6791 (m-80) outliers start: 50 outliers final: 27 residues processed: 371 average time/residue: 0.5785 time to fit residues: 242.0313 Evaluate side-chains 353 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 209 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 42 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 257 GLN A 310 GLN A 518 ASN A 519 ASN B 157 HIS B 257 GLN D 518 ASN D 519 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123916 restraints weight = 25011.650| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.18 r_work: 0.3191 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20064 Z= 0.126 Angle : 0.656 10.548 27248 Z= 0.328 Chirality : 0.042 0.169 3100 Planarity : 0.004 0.060 3460 Dihedral : 4.881 22.397 2672 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.55 % Allowed : 24.81 % Favored : 72.64 % 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: -0.69 (0.17), residues: 2440 helix: 0.56 (0.14), residues: 1400 sheet: -1.24 (0.57), residues: 56 loop : -1.92 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 45 TYR 0.033 0.002 TYR B 555 PHE 0.024 0.001 PHE A 553 TRP 0.009 0.001 TRP D 593 HIS 0.013 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00298 (20064) covalent geometry : angle 0.65616 (27248) hydrogen bonds : bond 0.03216 ( 820) hydrogen bonds : angle 3.89568 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7436.61 seconds wall clock time: 127 minutes 29.21 seconds (7649.21 seconds total)