Starting phenix.real_space_refine on Sun Sep 13 04:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dvz_8921/09_2026/6dvz_8921.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 B 12 2.79 5 C 13656 2.51 5 N 3452 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5193 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 625} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'FZ4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 6.26, per 1000 atoms: 0.30 Number of scatterers: 20976 At special positions: 0 Unit cell: (140.98, 140.98, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 O 3732 8.00 N 3452 7.00 C 13656 6.00 B 12 5.00 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 58.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.951A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.674A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.674A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.907A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.830A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.729A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.525A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.635A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.885A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.343A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.767A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.784A pdb=" N LEU A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.723A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.516A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 4.282A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 501 removed outlier: 3.697A pdb=" N LEU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.751A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 523 through 543 removed outlier: 3.816A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.733A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.152A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 607 removed outlier: 3.752A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.867A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.941A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.628A pdb=" N LEU A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.740A pdb=" N ARG A 696 " --> pdb=" O TRP A 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.951A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.673A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.674A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.907A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.830A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.729A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.526A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.636A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.884A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.342A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.767A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.784A pdb=" N LEU B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.723A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.516A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 4.282A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 501 removed outlier: 3.698A pdb=" N LEU B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.751A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 523 through 543 removed outlier: 3.815A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.732A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 removed outlier: 4.152A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 607 removed outlier: 3.753A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.867A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 666 removed outlier: 3.941A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 686 removed outlier: 3.627A pdb=" N LEU B 676 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 706 removed outlier: 3.740A pdb=" N ARG B 696 " --> pdb=" O TRP B 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'C' and resid 120 through 130 removed outlier: 3.951A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.673A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.675A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.941A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.830A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 removed outlier: 3.729A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.526A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.636A pdb=" N LEU C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.886A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.343A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.584A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.767A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.784A pdb=" N LEU C 370 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.722A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.516A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 4.282A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 501 removed outlier: 3.697A pdb=" N LEU C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.750A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 523 through 543 removed outlier: 3.815A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 561 Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.732A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 582 removed outlier: 4.152A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 607 removed outlier: 3.752A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 634 removed outlier: 3.867A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 666 removed outlier: 3.941A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.627A pdb=" N LEU C 676 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 706 removed outlier: 3.740A pdb=" N ARG C 696 " --> pdb=" O TRP C 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.951A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.673A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.674A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.906A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.830A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.729A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.525A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.635A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.884A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.343A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 removed outlier: 3.585A pdb=" N GLU D 334 " --> pdb=" O TRP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.767A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.784A pdb=" N LEU D 370 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.723A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.516A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 4.282A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 501 removed outlier: 3.698A pdb=" N LEU D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 507 removed outlier: 3.752A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 Processing helix chain 'D' and resid 523 through 543 removed outlier: 3.816A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 561 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.732A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 582 removed outlier: 4.152A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 607 removed outlier: 3.753A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 634 removed outlier: 3.867A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 666 removed outlier: 3.941A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 686 removed outlier: 3.627A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 706 removed outlier: 3.740A pdb=" N ARG D 696 " --> pdb=" O TRP D 692 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.556A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 386 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 735 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 381 through 382 removed outlier: 3.556A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 386 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 735 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.556A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 386 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 735 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.556A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER D 386 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 735 " --> pdb=" O SER D 386 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2028 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: 3.13 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6504 1.34 - 1.46: 4755 1.46 - 1.58: 9957 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21420 Sorted by residual: bond pdb=" CA SER A 515 " pdb=" C SER A 515 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.48e+00 bond pdb=" CA SER C 515 " pdb=" C SER C 515 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.48e+00 bond pdb=" CA SER B 515 " pdb=" C SER B 515 " ideal model delta sigma weight residual 1.523 1.560 -0.036 1.34e-02 5.57e+03 7.41e+00 bond pdb=" CA SER D 515 " pdb=" C SER D 515 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.34e-02 5.57e+03 7.27e+00 bond pdb=" CB GLN D 346 " pdb=" CG GLN D 346 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.93e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27394 2.49 - 4.99: 1247 4.99 - 7.48: 214 7.48 - 9.98: 81 9.98 - 12.47: 12 Bond angle restraints: 28948 Sorted by residual: angle pdb=" N PRO D 756 " pdb=" CA PRO D 756 " pdb=" CB PRO D 756 " ideal model delta sigma weight residual 103.15 110.78 -7.63 9.70e-01 1.06e+00 6.19e+01 angle pdb=" N PRO B 756 " pdb=" CA PRO B 756 " pdb=" CB PRO B 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO C 756 " pdb=" CA PRO C 756 " pdb=" CB PRO C 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO A 756 " pdb=" CA PRO A 756 " pdb=" CB PRO A 756 " ideal model delta sigma weight residual 103.15 110.74 -7.59 9.70e-01 1.06e+00 6.13e+01 angle pdb=" N PRO C 758 " pdb=" CA PRO C 758 " pdb=" CB PRO C 758 " ideal model delta sigma weight residual 103.25 111.21 -7.96 1.05e+00 9.07e-01 5.75e+01 ... (remaining 28943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 12292 23.85 - 47.71: 404 47.71 - 71.56: 24 71.56 - 95.42: 20 95.42 - 119.27: 4 Dihedral angle restraints: 12744 sinusoidal: 5160 harmonic: 7584 Sorted by residual: dihedral pdb=" CA GLU A 423 " pdb=" C GLU A 423 " pdb=" N PRO A 424 " pdb=" CA PRO A 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU D 423 " pdb=" C GLU D 423 " pdb=" N PRO D 424 " pdb=" CA PRO D 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU C 423 " pdb=" C GLU C 423 " pdb=" N PRO C 424 " pdb=" CA PRO C 424 " ideal model delta harmonic sigma weight residual -180.00 -120.92 -59.08 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2857 0.080 - 0.161: 371 0.161 - 0.241: 45 0.241 - 0.321: 15 0.321 - 0.402: 4 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE C 644 " pdb=" CA ILE C 644 " pdb=" CG1 ILE C 644 " pdb=" CG2 ILE C 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE B 644 " pdb=" CA ILE B 644 " pdb=" CG1 ILE B 644 " pdb=" CG2 ILE B 644 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3289 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 423 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 423 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 424 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 424 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 424 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 423 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO A 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.048 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5695 2.79 - 3.32: 19537 3.32 - 3.85: 31985 3.85 - 4.37: 36192 4.37 - 4.90: 59210 Nonbonded interactions: 152619 Sorted by model distance: nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.266 3.040 nonbonded pdb=" O THR B 167 " pdb=" OG1 THR B 209 " model vdw 2.270 3.040 ... (remaining 152614 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: 0.07 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.470 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 21432 Z= 0.391 Angle : 1.270 12.469 28948 Z= 0.678 Chirality : 0.062 0.402 3292 Planarity : 0.007 0.089 3600 Dihedral : 12.540 119.270 7816 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.78 % Allowed : 16.63 % Favored : 82.59 % Rotamer: Outliers : 0.18 % Allowed : 5.88 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.48 % 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: -5.86 (0.12), residues: 2556 helix: -3.94 (0.08), residues: 1220 sheet: -5.15 (0.43), residues: 52 loop : -3.82 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 375 TYR 0.032 0.004 TYR C 661 PHE 0.035 0.004 PHE A 259 TRP 0.018 0.003 TRP B 331 HIS 0.011 0.003 HIS D 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.39 (21420) covalent geometry : angle 1.27023 / 0.68 (28948) hydrogen bonds : bond 0.31227 / 20.43 ( 696) hydrogen bonds : angle 10.52292 / 7.34 ( 2028) Misc. bond : bond 0.00585 / 0.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 704 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8020 (pmt-80) cc_final: 0.7361 (ptp-170) REVERT: A 230 ILE cc_start: 0.9304 (mt) cc_final: 0.8885 (mt) REVERT: A 309 ASP cc_start: 0.8374 (m-30) cc_final: 0.7936 (t0) REVERT: A 321 TYR cc_start: 0.8695 (t80) cc_final: 0.8427 (t80) REVERT: A 414 ASP cc_start: 0.7582 (m-30) cc_final: 0.6947 (t0) REVERT: A 440 MET cc_start: 0.8536 (mtt) cc_final: 0.8281 (mmt) REVERT: A 580 GLN cc_start: 0.8757 (tt0) cc_final: 0.8478 (tt0) REVERT: A 705 LYS cc_start: 0.9533 (ttmt) cc_final: 0.9040 (ttmm) REVERT: B 150 ARG cc_start: 0.8020 (pmt-80) cc_final: 0.7357 (ptp-170) REVERT: B 230 ILE cc_start: 0.9306 (mt) cc_final: 0.8889 (mt) REVERT: B 309 ASP cc_start: 0.8379 (m-30) cc_final: 0.7943 (t0) REVERT: B 321 TYR cc_start: 0.8694 (t80) cc_final: 0.8437 (t80) REVERT: B 414 ASP cc_start: 0.7551 (m-30) cc_final: 0.6912 (t0) REVERT: B 440 MET cc_start: 0.8528 (mtt) cc_final: 0.8286 (mmt) REVERT: B 538 PHE cc_start: 0.7209 (t80) cc_final: 0.7005 (t80) REVERT: B 580 GLN cc_start: 0.8752 (tt0) cc_final: 0.8452 (tt0) REVERT: B 705 LYS cc_start: 0.9532 (ttmt) cc_final: 0.9039 (ttmm) REVERT: C 150 ARG cc_start: 0.8013 (pmt-80) cc_final: 0.7356 (ptp-170) REVERT: C 230 ILE cc_start: 0.9309 (mt) cc_final: 0.8886 (mt) REVERT: C 309 ASP cc_start: 0.8399 (m-30) cc_final: 0.7945 (t0) REVERT: C 321 TYR cc_start: 0.8687 (t80) cc_final: 0.8430 (t80) REVERT: C 414 ASP cc_start: 0.7555 (m-30) cc_final: 0.6927 (t0) REVERT: C 440 MET cc_start: 0.8507 (mtt) cc_final: 0.8280 (mmt) REVERT: C 538 PHE cc_start: 0.7190 (t80) cc_final: 0.6986 (t80) REVERT: C 705 LYS cc_start: 0.9534 (ttmt) cc_final: 0.9039 (ttmm) REVERT: D 150 ARG cc_start: 0.8011 (pmt-80) cc_final: 0.7359 (ptp-170) REVERT: D 230 ILE cc_start: 0.9303 (mt) cc_final: 0.8887 (mt) REVERT: D 309 ASP cc_start: 0.8391 (m-30) cc_final: 0.7945 (t0) REVERT: D 321 TYR cc_start: 0.8690 (t80) cc_final: 0.8421 (t80) REVERT: D 414 ASP cc_start: 0.7566 (m-30) cc_final: 0.6922 (t0) REVERT: D 440 MET cc_start: 0.8504 (mtt) cc_final: 0.8273 (mmt) REVERT: D 538 PHE cc_start: 0.7225 (t80) cc_final: 0.7015 (t80) REVERT: D 580 GLN cc_start: 0.8748 (tt0) cc_final: 0.8472 (tt0) REVERT: D 705 LYS cc_start: 0.9538 (ttmt) cc_final: 0.9041 (ttmm) outliers start: 4 outliers final: 0 residues processed: 708 average time/residue: 0.1455 time to fit residues: 160.4150 Evaluate side-chains 457 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 735 ASN B 645 GLN B 735 ASN C 580 GLN C 735 ASN D 645 GLN D 735 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094734 restraints weight = 56886.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097239 restraints weight = 31845.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098932 restraints weight = 21293.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100031 restraints weight = 16057.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100822 restraints weight = 13266.369| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21432 Z= 0.155 Angle : 0.787 9.059 28948 Z= 0.406 Chirality : 0.044 0.221 3292 Planarity : 0.005 0.068 3600 Dihedral : 9.165 99.591 2836 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.71 % Favored : 85.13 % Rotamer: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -4.45 (0.14), residues: 2556 helix: -2.37 (0.11), residues: 1352 sheet: -4.11 (0.69), residues: 52 loop : -3.63 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.020 0.002 TYR A 540 PHE 0.020 0.002 PHE A 538 TRP 0.012 0.001 TRP D 481 HIS 0.007 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (21420) covalent geometry : angle 0.78659 / 0.41 (28948) hydrogen bonds : bond 0.05232 / 3.46 ( 696) hydrogen bonds : angle 5.24493 / 3.69 ( 2028) Misc. bond : bond 0.00152 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 616 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.7901 (pmt-80) cc_final: 0.7393 (ptp-170) REVERT: A 298 ASN cc_start: 0.9324 (p0) cc_final: 0.9040 (p0) REVERT: A 309 ASP cc_start: 0.8245 (m-30) cc_final: 0.7798 (t0) REVERT: A 321 TYR cc_start: 0.8613 (t80) cc_final: 0.8351 (t80) REVERT: A 440 MET cc_start: 0.8792 (mtt) cc_final: 0.8306 (mmp) REVERT: A 663 ILE cc_start: 0.9731 (tp) cc_final: 0.9530 (tp) REVERT: A 670 LEU cc_start: 0.9602 (mm) cc_final: 0.9273 (tp) REVERT: A 679 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 150 ARG cc_start: 0.7901 (pmt-80) cc_final: 0.7399 (ptp-170) REVERT: B 298 ASN cc_start: 0.9319 (p0) cc_final: 0.9059 (p0) REVERT: B 309 ASP cc_start: 0.8224 (m-30) cc_final: 0.7801 (t0) REVERT: B 321 TYR cc_start: 0.8637 (t80) cc_final: 0.8386 (t80) REVERT: B 347 LEU cc_start: 0.9565 (tp) cc_final: 0.9364 (tt) REVERT: B 440 MET cc_start: 0.8785 (mtt) cc_final: 0.8297 (mmp) REVERT: B 538 PHE cc_start: 0.7293 (t80) cc_final: 0.7062 (t80) REVERT: B 663 ILE cc_start: 0.9737 (tp) cc_final: 0.9533 (tp) REVERT: B 670 LEU cc_start: 0.9613 (mm) cc_final: 0.9285 (tp) REVERT: C 150 ARG cc_start: 0.7910 (pmt-80) cc_final: 0.7403 (ptp-170) REVERT: C 298 ASN cc_start: 0.9314 (p0) cc_final: 0.9066 (p0) REVERT: C 309 ASP cc_start: 0.8221 (m-30) cc_final: 0.7800 (t0) REVERT: C 321 TYR cc_start: 0.8640 (t80) cc_final: 0.8382 (t80) REVERT: C 347 LEU cc_start: 0.9577 (tp) cc_final: 0.9369 (tt) REVERT: C 440 MET cc_start: 0.8785 (mtt) cc_final: 0.8285 (mmp) REVERT: C 538 PHE cc_start: 0.7290 (t80) cc_final: 0.7062 (t80) REVERT: C 663 ILE cc_start: 0.9734 (tp) cc_final: 0.9530 (tp) REVERT: C 670 LEU cc_start: 0.9601 (mm) cc_final: 0.9275 (tp) REVERT: D 150 ARG cc_start: 0.7892 (pmt-80) cc_final: 0.7391 (ptp-170) REVERT: D 298 ASN cc_start: 0.9324 (p0) cc_final: 0.9037 (p0) REVERT: D 309 ASP cc_start: 0.8235 (m-30) cc_final: 0.7791 (t0) REVERT: D 321 TYR cc_start: 0.8620 (t80) cc_final: 0.8364 (t80) REVERT: D 440 MET cc_start: 0.8786 (mtt) cc_final: 0.8298 (mmp) REVERT: D 538 PHE cc_start: 0.7283 (t80) cc_final: 0.7061 (t80) REVERT: D 663 ILE cc_start: 0.9729 (tp) cc_final: 0.9529 (tp) REVERT: D 670 LEU cc_start: 0.9582 (mm) cc_final: 0.9306 (tp) outliers start: 2 outliers final: 0 residues processed: 618 average time/residue: 0.1372 time to fit residues: 135.6096 Evaluate side-chains 445 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 109 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 645 GLN C 274 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 645 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095456 restraints weight = 56032.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098032 restraints weight = 31631.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099757 restraints weight = 21147.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100835 restraints weight = 15879.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101730 restraints weight = 13083.492| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21432 Z= 0.153 Angle : 0.715 7.941 28948 Z= 0.371 Chirality : 0.043 0.225 3292 Planarity : 0.005 0.070 3600 Dihedral : 8.301 80.679 2836 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.43 % Favored : 83.41 % Rotamer: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -3.39 (0.15), residues: 2556 helix: -1.31 (0.13), residues: 1368 sheet: -3.90 (0.71), residues: 52 loop : -3.41 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 226 TYR 0.017 0.002 TYR C 540 PHE 0.019 0.002 PHE B 259 TRP 0.009 0.001 TRP D 521 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21420) covalent geometry : angle 0.71511 / 0.37 (28948) hydrogen bonds : bond 0.03856 / 2.54 ( 696) hydrogen bonds : angle 4.52995 / 3.19 ( 2028) Misc. bond : bond 0.00150 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 573 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8001 (pmt-80) cc_final: 0.7463 (ptp-170) REVERT: A 309 ASP cc_start: 0.8281 (m-30) cc_final: 0.7847 (t0) REVERT: A 311 LYS cc_start: 0.8487 (mttt) cc_final: 0.7336 (tmtt) REVERT: A 321 TYR cc_start: 0.8760 (t80) cc_final: 0.8538 (t80) REVERT: A 405 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 414 ASP cc_start: 0.7535 (m-30) cc_final: 0.6815 (t0) REVERT: A 440 MET cc_start: 0.8677 (mtt) cc_final: 0.8261 (mmp) REVERT: A 538 PHE cc_start: 0.7321 (t80) cc_final: 0.7085 (t80) REVERT: B 150 ARG cc_start: 0.7979 (pmt-80) cc_final: 0.7451 (ptp-170) REVERT: B 309 ASP cc_start: 0.8278 (m-30) cc_final: 0.7848 (t0) REVERT: B 311 LYS cc_start: 0.8490 (mttt) cc_final: 0.7346 (tmtt) REVERT: B 321 TYR cc_start: 0.8756 (t80) cc_final: 0.8548 (t80) REVERT: B 414 ASP cc_start: 0.7511 (m-30) cc_final: 0.6820 (t0) REVERT: B 440 MET cc_start: 0.8667 (mtt) cc_final: 0.8252 (mmp) REVERT: C 150 ARG cc_start: 0.7985 (pmt-80) cc_final: 0.7452 (ptp-170) REVERT: C 309 ASP cc_start: 0.8262 (m-30) cc_final: 0.7837 (t0) REVERT: C 311 LYS cc_start: 0.8484 (mttt) cc_final: 0.7343 (tmtt) REVERT: C 321 TYR cc_start: 0.8769 (t80) cc_final: 0.8560 (t80) REVERT: C 414 ASP cc_start: 0.7499 (m-30) cc_final: 0.6801 (t0) REVERT: C 440 MET cc_start: 0.8662 (mtt) cc_final: 0.8238 (mmp) REVERT: D 150 ARG cc_start: 0.7978 (pmt-80) cc_final: 0.7462 (ptp-170) REVERT: D 309 ASP cc_start: 0.8276 (m-30) cc_final: 0.7845 (t0) REVERT: D 311 LYS cc_start: 0.8481 (mttt) cc_final: 0.7342 (tmtt) REVERT: D 321 TYR cc_start: 0.8771 (t80) cc_final: 0.8549 (t80) REVERT: D 405 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8201 (mt-10) REVERT: D 414 ASP cc_start: 0.7525 (m-30) cc_final: 0.6806 (t0) REVERT: D 440 MET cc_start: 0.8660 (mtt) cc_final: 0.8230 (mmp) REVERT: D 712 ARG cc_start: 0.7201 (pmt-80) cc_final: 0.6923 (tmm160) outliers start: 2 outliers final: 0 residues processed: 575 average time/residue: 0.1298 time to fit residues: 121.4259 Evaluate side-chains 391 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 251 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 339 ASN B 645 GLN B 671 ASN C 178 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 645 GLN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096322 restraints weight = 56100.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098901 restraints weight = 31617.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100668 restraints weight = 21026.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101865 restraints weight = 15719.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102704 restraints weight = 12808.720| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21432 Z= 0.128 Angle : 0.680 7.977 28948 Z= 0.351 Chirality : 0.042 0.223 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.599 55.493 2836 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.48 % Favored : 85.37 % Rotamer: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.16 % 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: -2.96 (0.16), residues: 2556 helix: -0.85 (0.13), residues: 1384 sheet: -3.75 (0.74), residues: 52 loop : -3.40 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.021 0.001 TYR B 451 PHE 0.020 0.001 PHE B 590 TRP 0.006 0.001 TRP A 481 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21420) covalent geometry : angle 0.68023 / 0.35 (28948) hydrogen bonds : bond 0.03090 / 2.06 ( 696) hydrogen bonds : angle 4.13557 / 2.89 ( 2028) Misc. bond : bond 0.00148 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 561 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.7998 (m-30) cc_final: 0.7027 (m-30) REVERT: A 309 ASP cc_start: 0.8226 (m-30) cc_final: 0.7953 (t0) REVERT: A 311 LYS cc_start: 0.8400 (mttt) cc_final: 0.7677 (tmtt) REVERT: A 414 ASP cc_start: 0.7546 (m-30) cc_final: 0.6895 (t0) REVERT: A 440 MET cc_start: 0.8612 (mtt) cc_final: 0.8182 (mmt) REVERT: A 555 MET cc_start: 0.8426 (tmm) cc_final: 0.8135 (tmm) REVERT: A 717 MET cc_start: 0.7335 (mpp) cc_final: 0.7012 (mtt) REVERT: B 293 ASP cc_start: 0.8159 (m-30) cc_final: 0.7944 (m-30) REVERT: B 309 ASP cc_start: 0.8238 (m-30) cc_final: 0.7957 (t0) REVERT: B 311 LYS cc_start: 0.8372 (mttt) cc_final: 0.7619 (tmtt) REVERT: B 414 ASP cc_start: 0.7563 (m-30) cc_final: 0.6896 (t0) REVERT: B 440 MET cc_start: 0.8602 (mtt) cc_final: 0.8170 (mmt) REVERT: B 538 PHE cc_start: 0.7214 (t80) cc_final: 0.6998 (t80) REVERT: B 712 ARG cc_start: 0.7129 (pmt-80) cc_final: 0.6880 (tmm160) REVERT: B 717 MET cc_start: 0.7399 (mpp) cc_final: 0.7008 (mtt) REVERT: B 727 ASP cc_start: 0.7191 (p0) cc_final: 0.6115 (p0) REVERT: C 293 ASP cc_start: 0.8009 (m-30) cc_final: 0.7045 (m-30) REVERT: C 309 ASP cc_start: 0.8219 (m-30) cc_final: 0.7954 (t0) REVERT: C 311 LYS cc_start: 0.8360 (mttt) cc_final: 0.7620 (tmtt) REVERT: C 414 ASP cc_start: 0.7530 (m-30) cc_final: 0.6875 (t0) REVERT: C 440 MET cc_start: 0.8594 (mtt) cc_final: 0.8155 (mmt) REVERT: C 538 PHE cc_start: 0.7224 (t80) cc_final: 0.7006 (t80) REVERT: C 712 ARG cc_start: 0.7126 (pmt-80) cc_final: 0.6873 (tmm160) REVERT: C 717 MET cc_start: 0.7415 (mpp) cc_final: 0.7019 (mtt) REVERT: C 727 ASP cc_start: 0.7086 (p0) cc_final: 0.6051 (p0) REVERT: D 293 ASP cc_start: 0.7983 (m-30) cc_final: 0.7014 (m-30) REVERT: D 309 ASP cc_start: 0.8237 (m-30) cc_final: 0.7961 (t0) REVERT: D 311 LYS cc_start: 0.8394 (mttt) cc_final: 0.7684 (tmtt) REVERT: D 414 ASP cc_start: 0.7556 (m-30) cc_final: 0.6882 (t0) REVERT: D 440 MET cc_start: 0.8607 (mtt) cc_final: 0.8172 (mmt) REVERT: D 538 PHE cc_start: 0.7213 (t80) cc_final: 0.6997 (t80) REVERT: D 578 MET cc_start: 0.7572 (mtm) cc_final: 0.6195 (mtm) REVERT: D 717 MET cc_start: 0.7328 (mpp) cc_final: 0.6975 (mtt) REVERT: D 727 ASP cc_start: 0.7057 (p0) cc_final: 0.6045 (p0) outliers start: 1 outliers final: 0 residues processed: 562 average time/residue: 0.1292 time to fit residues: 118.6936 Evaluate side-chains 402 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 164 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095622 restraints weight = 56232.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098268 restraints weight = 31975.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100062 restraints weight = 21352.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101255 restraints weight = 15935.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102137 restraints weight = 12989.840| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21432 Z= 0.140 Angle : 0.688 7.824 28948 Z= 0.352 Chirality : 0.043 0.224 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.299 49.151 2836 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.30 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -2.56 (0.16), residues: 2556 helix: -0.51 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -3.30 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.015 0.001 TYR A 540 PHE 0.020 0.001 PHE D 654 TRP 0.006 0.001 TRP A 739 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21420) covalent geometry : angle 0.68798 / 0.35 (28948) hydrogen bonds : bond 0.03159 / 2.11 ( 696) hydrogen bonds : angle 4.21168 / 2.95 ( 2028) Misc. bond : bond 0.00130 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLU cc_start: 0.7387 (pm20) cc_final: 0.6876 (pm20) REVERT: A 293 ASP cc_start: 0.7775 (m-30) cc_final: 0.7425 (m-30) REVERT: A 309 ASP cc_start: 0.8359 (m-30) cc_final: 0.7983 (t0) REVERT: A 414 ASP cc_start: 0.7665 (m-30) cc_final: 0.6940 (t0) REVERT: A 440 MET cc_start: 0.8625 (mtt) cc_final: 0.8227 (mmt) REVERT: A 538 PHE cc_start: 0.7424 (t80) cc_final: 0.7222 (t80) REVERT: A 555 MET cc_start: 0.8507 (tmm) cc_final: 0.8061 (tmm) REVERT: A 717 MET cc_start: 0.7580 (mpp) cc_final: 0.7053 (mtt) REVERT: B 293 ASP cc_start: 0.8040 (m-30) cc_final: 0.7581 (m-30) REVERT: B 309 ASP cc_start: 0.8360 (m-30) cc_final: 0.7992 (t0) REVERT: B 414 ASP cc_start: 0.7665 (m-30) cc_final: 0.6949 (t0) REVERT: B 440 MET cc_start: 0.8621 (mtt) cc_final: 0.8231 (mmt) REVERT: B 717 MET cc_start: 0.7557 (mpp) cc_final: 0.7033 (mtt) REVERT: C 263 GLU cc_start: 0.7369 (pm20) cc_final: 0.6868 (pm20) REVERT: C 293 ASP cc_start: 0.7783 (m-30) cc_final: 0.7454 (m-30) REVERT: C 309 ASP cc_start: 0.8351 (m-30) cc_final: 0.7982 (t0) REVERT: C 414 ASP cc_start: 0.7654 (m-30) cc_final: 0.6931 (t0) REVERT: C 440 MET cc_start: 0.8617 (mtt) cc_final: 0.8217 (mmt) REVERT: C 574 MET cc_start: 0.8712 (ppp) cc_final: 0.8231 (ppp) REVERT: C 578 MET cc_start: 0.7824 (mtm) cc_final: 0.7616 (mtm) REVERT: C 717 MET cc_start: 0.7578 (mpp) cc_final: 0.7053 (mtt) REVERT: D 263 GLU cc_start: 0.7374 (pm20) cc_final: 0.6880 (pm20) REVERT: D 293 ASP cc_start: 0.7767 (m-30) cc_final: 0.7429 (m-30) REVERT: D 309 ASP cc_start: 0.8374 (m-30) cc_final: 0.7985 (t0) REVERT: D 414 ASP cc_start: 0.7657 (m-30) cc_final: 0.6928 (t0) REVERT: D 440 MET cc_start: 0.8611 (mtt) cc_final: 0.8220 (mmt) REVERT: D 717 MET cc_start: 0.7522 (mpp) cc_final: 0.7028 (mtt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1334 time to fit residues: 118.2326 Evaluate side-chains 398 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095891 restraints weight = 55466.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098427 restraints weight = 31992.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100159 restraints weight = 21642.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101342 restraints weight = 16326.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102172 restraints weight = 13343.896| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21432 Z= 0.133 Angle : 0.707 10.771 28948 Z= 0.357 Chirality : 0.043 0.224 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.093 51.142 2836 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.51 % Favored : 85.33 % Rotamer: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -2.40 (0.16), residues: 2556 helix: -0.40 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -3.21 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.022 0.001 TYR D 451 PHE 0.018 0.001 PHE D 654 TRP 0.006 0.001 TRP A 739 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21420) covalent geometry : angle 0.70721 / 0.36 (28948) hydrogen bonds : bond 0.03009 / 2.00 ( 696) hydrogen bonds : angle 4.16565 / 2.92 ( 2028) Misc. bond : bond 0.00217 / 0.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 548 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 263 GLU cc_start: 0.7262 (pm20) cc_final: 0.6719 (pm20) REVERT: A 293 ASP cc_start: 0.7722 (m-30) cc_final: 0.7321 (m-30) REVERT: A 304 VAL cc_start: 0.9506 (t) cc_final: 0.9300 (p) REVERT: A 309 ASP cc_start: 0.8346 (m-30) cc_final: 0.8021 (t0) REVERT: A 414 ASP cc_start: 0.7542 (m-30) cc_final: 0.7059 (t0) REVERT: A 440 MET cc_start: 0.8632 (mtt) cc_final: 0.8212 (mmt) REVERT: A 538 PHE cc_start: 0.7374 (t80) cc_final: 0.7140 (t80) REVERT: A 555 MET cc_start: 0.8544 (tmm) cc_final: 0.7949 (tmm) REVERT: A 578 MET cc_start: 0.8695 (tpp) cc_final: 0.8077 (tpp) REVERT: A 717 MET cc_start: 0.7507 (mpp) cc_final: 0.7063 (mtt) REVERT: A 727 ASP cc_start: 0.6961 (p0) cc_final: 0.6362 (p0) REVERT: B 255 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 304 VAL cc_start: 0.9510 (t) cc_final: 0.9297 (p) REVERT: B 309 ASP cc_start: 0.8359 (m-30) cc_final: 0.8030 (t0) REVERT: B 414 ASP cc_start: 0.7566 (m-30) cc_final: 0.7065 (t0) REVERT: B 440 MET cc_start: 0.8633 (mtt) cc_final: 0.8210 (mmt) REVERT: B 538 PHE cc_start: 0.7393 (t80) cc_final: 0.7136 (t80) REVERT: B 672 MET cc_start: 0.8699 (tpp) cc_final: 0.8365 (tpt) REVERT: B 717 MET cc_start: 0.7456 (mpp) cc_final: 0.7069 (mtt) REVERT: C 255 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 263 GLU cc_start: 0.7235 (pm20) cc_final: 0.6697 (pm20) REVERT: C 293 ASP cc_start: 0.7772 (m-30) cc_final: 0.7381 (m-30) REVERT: C 304 VAL cc_start: 0.9507 (t) cc_final: 0.9299 (p) REVERT: C 309 ASP cc_start: 0.8360 (m-30) cc_final: 0.8021 (t0) REVERT: C 321 TYR cc_start: 0.8769 (t80) cc_final: 0.8546 (t80) REVERT: C 414 ASP cc_start: 0.7534 (m-30) cc_final: 0.7032 (t0) REVERT: C 440 MET cc_start: 0.8637 (mtt) cc_final: 0.8206 (mmt) REVERT: C 538 PHE cc_start: 0.7421 (t80) cc_final: 0.7150 (t80) REVERT: C 574 MET cc_start: 0.8738 (ppp) cc_final: 0.8075 (ppp) REVERT: C 717 MET cc_start: 0.7462 (mpp) cc_final: 0.7073 (mtt) REVERT: D 255 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 263 GLU cc_start: 0.7259 (pm20) cc_final: 0.6713 (pm20) REVERT: D 293 ASP cc_start: 0.7714 (m-30) cc_final: 0.7305 (m-30) REVERT: D 304 VAL cc_start: 0.9503 (t) cc_final: 0.9287 (p) REVERT: D 309 ASP cc_start: 0.8349 (m-30) cc_final: 0.8011 (t0) REVERT: D 321 TYR cc_start: 0.8783 (t80) cc_final: 0.8557 (t80) REVERT: D 414 ASP cc_start: 0.7535 (m-30) cc_final: 0.7031 (t0) REVERT: D 440 MET cc_start: 0.8629 (mtt) cc_final: 0.8209 (mmt) REVERT: D 538 PHE cc_start: 0.7395 (t80) cc_final: 0.7134 (t80) REVERT: D 717 MET cc_start: 0.7439 (mpp) cc_final: 0.7055 (mtt) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.1348 time to fit residues: 119.9394 Evaluate side-chains 394 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 189 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094184 restraints weight = 56665.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096698 restraints weight = 32976.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098404 restraints weight = 22363.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099590 restraints weight = 16904.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100338 restraints weight = 13840.362| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21432 Z= 0.164 Angle : 0.739 8.890 28948 Z= 0.372 Chirality : 0.044 0.223 3292 Planarity : 0.005 0.074 3600 Dihedral : 7.247 51.148 2836 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.53 % Favored : 84.31 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % 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: -2.26 (0.17), residues: 2556 helix: -0.28 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -3.16 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.014 0.002 TYR A 540 PHE 0.029 0.002 PHE B 261 TRP 0.011 0.001 TRP B 692 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (21420) covalent geometry : angle 0.73946 / 0.37 (28948) hydrogen bonds : bond 0.03244 / 2.16 ( 696) hydrogen bonds : angle 4.26848 / 3.00 ( 2028) Misc. bond : bond 0.00177 / 0.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 255 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 293 ASP cc_start: 0.7810 (m-30) cc_final: 0.7598 (m-30) REVERT: A 304 VAL cc_start: 0.9514 (t) cc_final: 0.9286 (p) REVERT: A 309 ASP cc_start: 0.8333 (m-30) cc_final: 0.8007 (t0) REVERT: A 347 LEU cc_start: 0.9315 (tp) cc_final: 0.8977 (tt) REVERT: A 414 ASP cc_start: 0.7687 (m-30) cc_final: 0.7118 (t0) REVERT: A 440 MET cc_start: 0.8636 (mtt) cc_final: 0.8240 (mmt) REVERT: A 578 MET cc_start: 0.8459 (tpp) cc_final: 0.8169 (tpp) REVERT: A 717 MET cc_start: 0.7498 (mpp) cc_final: 0.7064 (mtt) REVERT: B 224 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 255 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 304 VAL cc_start: 0.9505 (t) cc_final: 0.9303 (p) REVERT: B 309 ASP cc_start: 0.8351 (m-30) cc_final: 0.8000 (t0) REVERT: B 405 GLU cc_start: 0.8659 (pt0) cc_final: 0.8405 (pt0) REVERT: B 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.7123 (t0) REVERT: B 440 MET cc_start: 0.8626 (mtt) cc_final: 0.8240 (mmt) REVERT: B 717 MET cc_start: 0.7492 (mpp) cc_final: 0.7002 (mtt) REVERT: C 224 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 255 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 293 ASP cc_start: 0.7802 (m-30) cc_final: 0.7588 (m-30) REVERT: C 304 VAL cc_start: 0.9516 (t) cc_final: 0.9264 (p) REVERT: C 309 ASP cc_start: 0.8338 (m-30) cc_final: 0.8008 (t0) REVERT: C 321 TYR cc_start: 0.8944 (t80) cc_final: 0.8690 (t80) REVERT: C 347 LEU cc_start: 0.9339 (tp) cc_final: 0.9021 (tt) REVERT: C 405 GLU cc_start: 0.8657 (pt0) cc_final: 0.8410 (pt0) REVERT: C 414 ASP cc_start: 0.7659 (m-30) cc_final: 0.7105 (t0) REVERT: C 440 MET cc_start: 0.8626 (mtt) cc_final: 0.8231 (mmt) REVERT: C 578 MET cc_start: 0.8116 (mtm) cc_final: 0.7829 (mtm) REVERT: C 717 MET cc_start: 0.7539 (mpp) cc_final: 0.6999 (mtt) REVERT: D 224 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 255 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 309 ASP cc_start: 0.8328 (m-30) cc_final: 0.8008 (t0) REVERT: D 321 TYR cc_start: 0.8950 (t80) cc_final: 0.8723 (t80) REVERT: D 347 LEU cc_start: 0.9327 (tp) cc_final: 0.9039 (tt) REVERT: D 414 ASP cc_start: 0.7635 (m-30) cc_final: 0.7065 (t0) REVERT: D 440 MET cc_start: 0.8625 (mtt) cc_final: 0.8249 (mmt) REVERT: D 717 MET cc_start: 0.7492 (mpp) cc_final: 0.6976 (mtt) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.1342 time to fit residues: 112.6428 Evaluate side-chains 386 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 251 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 580 GLN B 255 GLN B 339 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS C 645 GLN D 255 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096692 restraints weight = 56022.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099275 restraints weight = 32204.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101072 restraints weight = 21689.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102251 restraints weight = 16252.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103100 restraints weight = 13293.850| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21432 Z= 0.122 Angle : 0.714 8.375 28948 Z= 0.355 Chirality : 0.042 0.222 3292 Planarity : 0.005 0.073 3600 Dihedral : 7.096 49.304 2836 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.87 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.04 % 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: -2.10 (0.17), residues: 2556 helix: -0.18 (0.14), residues: 1404 sheet: -4.02 (0.67), residues: 52 loop : -2.95 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.019 0.001 TYR A 650 PHE 0.031 0.001 PHE B 261 TRP 0.009 0.001 TRP B 521 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21420) covalent geometry : angle 0.71358 / 0.36 (28948) hydrogen bonds : bond 0.02890 / 1.91 ( 696) hydrogen bonds : angle 4.10867 / 2.90 ( 2028) Misc. bond : bond 0.00156 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.8809 (tm130) cc_final: 0.8531 (tm-30) REVERT: A 304 VAL cc_start: 0.9491 (t) cc_final: 0.9257 (p) REVERT: A 309 ASP cc_start: 0.8262 (m-30) cc_final: 0.7950 (t0) REVERT: A 311 LYS cc_start: 0.8424 (mttt) cc_final: 0.7607 (tmtt) REVERT: A 347 LEU cc_start: 0.9283 (tp) cc_final: 0.8970 (tt) REVERT: A 405 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 414 ASP cc_start: 0.7447 (m-30) cc_final: 0.7117 (t0) REVERT: A 440 MET cc_start: 0.8632 (mtt) cc_final: 0.8209 (mmp) REVERT: A 555 MET cc_start: 0.8625 (tmm) cc_final: 0.8222 (tmm) REVERT: A 578 MET cc_start: 0.8383 (tpp) cc_final: 0.8158 (tpp) REVERT: A 634 LYS cc_start: 0.9223 (mtmt) cc_final: 0.9001 (mtmm) REVERT: A 704 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 706 MET cc_start: 0.8414 (tpp) cc_final: 0.7671 (tpp) REVERT: A 717 MET cc_start: 0.7494 (mpp) cc_final: 0.7065 (mtt) REVERT: B 255 GLN cc_start: 0.8837 (tm130) cc_final: 0.8584 (tm-30) REVERT: B 309 ASP cc_start: 0.8257 (m-30) cc_final: 0.7948 (t0) REVERT: B 311 LYS cc_start: 0.8442 (mttt) cc_final: 0.7656 (tmtt) REVERT: B 405 GLU cc_start: 0.8667 (pt0) cc_final: 0.8424 (pt0) REVERT: B 414 ASP cc_start: 0.7437 (m-30) cc_final: 0.7140 (t0) REVERT: B 440 MET cc_start: 0.8592 (mtt) cc_final: 0.8154 (mmp) REVERT: B 515 SER cc_start: 0.8379 (m) cc_final: 0.7129 (p) REVERT: B 519 ASP cc_start: 0.8095 (m-30) cc_final: 0.7838 (m-30) REVERT: B 594 TYR cc_start: 0.9140 (t80) cc_final: 0.8938 (t80) REVERT: B 704 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8181 (tm-30) REVERT: B 706 MET cc_start: 0.8428 (tpp) cc_final: 0.7708 (tpp) REVERT: B 717 MET cc_start: 0.7440 (mpp) cc_final: 0.7063 (mtt) REVERT: C 255 GLN cc_start: 0.8833 (tm130) cc_final: 0.8548 (tm-30) REVERT: C 304 VAL cc_start: 0.9482 (t) cc_final: 0.9229 (p) REVERT: C 309 ASP cc_start: 0.8244 (m-30) cc_final: 0.7951 (t0) REVERT: C 311 LYS cc_start: 0.8436 (mttt) cc_final: 0.7636 (tmtt) REVERT: C 347 LEU cc_start: 0.9296 (tp) cc_final: 0.9008 (tt) REVERT: C 405 GLU cc_start: 0.8673 (pt0) cc_final: 0.8430 (pt0) REVERT: C 414 ASP cc_start: 0.7447 (m-30) cc_final: 0.7130 (t0) REVERT: C 440 MET cc_start: 0.8569 (mtt) cc_final: 0.8133 (mmp) REVERT: C 522 PHE cc_start: 0.8661 (m-10) cc_final: 0.8405 (m-10) REVERT: C 704 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 706 MET cc_start: 0.8417 (tpp) cc_final: 0.7698 (tpp) REVERT: C 717 MET cc_start: 0.7415 (mpp) cc_final: 0.7012 (mtt) REVERT: D 255 GLN cc_start: 0.8812 (tm130) cc_final: 0.8533 (tm-30) REVERT: D 293 ASP cc_start: 0.8184 (m-30) cc_final: 0.7157 (m-30) REVERT: D 304 VAL cc_start: 0.9485 (t) cc_final: 0.9270 (p) REVERT: D 309 ASP cc_start: 0.8229 (m-30) cc_final: 0.7945 (t0) REVERT: D 311 LYS cc_start: 0.8435 (mttt) cc_final: 0.7655 (tmtt) REVERT: D 414 ASP cc_start: 0.7412 (m-30) cc_final: 0.7127 (t0) REVERT: D 440 MET cc_start: 0.8577 (mtt) cc_final: 0.8128 (mmp) REVERT: D 515 SER cc_start: 0.8353 (m) cc_final: 0.7101 (p) REVERT: D 519 ASP cc_start: 0.8058 (m-30) cc_final: 0.7794 (m-30) REVERT: D 706 MET cc_start: 0.8399 (tpp) cc_final: 0.7687 (tpp) REVERT: D 717 MET cc_start: 0.7465 (mpp) cc_final: 0.7025 (mtt) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.1330 time to fit residues: 115.3368 Evaluate side-chains 413 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 175 optimal weight: 3.9990 chunk 245 optimal weight: 0.1980 chunk 192 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS A 346 GLN B 255 GLN B 256 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN D 256 HIS ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093923 restraints weight = 57936.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096409 restraints weight = 34265.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098103 restraints weight = 23666.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099269 restraints weight = 18215.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100046 restraints weight = 15109.845| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21432 Z= 0.170 Angle : 0.754 7.760 28948 Z= 0.379 Chirality : 0.044 0.219 3292 Planarity : 0.005 0.075 3600 Dihedral : 7.150 49.490 2836 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.18 % Favored : 84.66 % Rotamer: Outliers : 0.04 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.04 % 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: -1.99 (0.17), residues: 2556 helix: -0.09 (0.14), residues: 1380 sheet: None (None), residues: 0 loop : -2.94 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.024 0.002 TYR B 451 PHE 0.033 0.002 PHE C 261 TRP 0.010 0.001 TRP B 692 HIS 0.006 0.002 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (21420) covalent geometry : angle 0.75425 / 0.38 (28948) hydrogen bonds : bond 0.03078 / 2.03 ( 696) hydrogen bonds : angle 4.22769 / 2.97 ( 2028) Misc. bond : bond 0.00137 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.8211 (m-30) cc_final: 0.8004 (t0) REVERT: A 321 TYR cc_start: 0.9040 (t80) cc_final: 0.8806 (t80) REVERT: A 405 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 414 ASP cc_start: 0.7771 (m-30) cc_final: 0.7295 (t0) REVERT: A 440 MET cc_start: 0.8621 (mtt) cc_final: 0.8261 (mmp) REVERT: A 555 MET cc_start: 0.8612 (tmm) cc_final: 0.8290 (tmm) REVERT: A 584 LEU cc_start: 0.9079 (mt) cc_final: 0.8871 (mp) REVERT: A 594 TYR cc_start: 0.9150 (t80) cc_final: 0.8847 (t80) REVERT: A 706 MET cc_start: 0.8514 (tpp) cc_final: 0.7863 (tpp) REVERT: A 717 MET cc_start: 0.7554 (mpp) cc_final: 0.7094 (mtt) REVERT: B 304 VAL cc_start: 0.9499 (t) cc_final: 0.9260 (p) REVERT: B 309 ASP cc_start: 0.8207 (m-30) cc_final: 0.8005 (t0) REVERT: B 321 TYR cc_start: 0.9031 (t80) cc_final: 0.8752 (t80) REVERT: B 405 GLU cc_start: 0.8692 (pt0) cc_final: 0.8422 (pt0) REVERT: B 414 ASP cc_start: 0.7740 (m-30) cc_final: 0.7257 (t0) REVERT: B 440 MET cc_start: 0.8623 (mtt) cc_final: 0.8313 (mmt) REVERT: B 555 MET cc_start: 0.8384 (tmm) cc_final: 0.8091 (tmm) REVERT: B 706 MET cc_start: 0.8517 (tpp) cc_final: 0.7857 (tpp) REVERT: B 717 MET cc_start: 0.7613 (mpp) cc_final: 0.7164 (mtt) REVERT: C 309 ASP cc_start: 0.8197 (m-30) cc_final: 0.7983 (t0) REVERT: C 405 GLU cc_start: 0.8677 (pt0) cc_final: 0.8418 (pt0) REVERT: C 414 ASP cc_start: 0.7732 (m-30) cc_final: 0.7248 (t0) REVERT: C 440 MET cc_start: 0.8581 (mtt) cc_final: 0.8270 (mmt) REVERT: C 521 TRP cc_start: 0.8717 (t60) cc_final: 0.7818 (t60) REVERT: C 555 MET cc_start: 0.8412 (tmm) cc_final: 0.8120 (tmm) REVERT: C 578 MET cc_start: 0.8468 (ptt) cc_final: 0.8267 (ttp) REVERT: C 706 MET cc_start: 0.8495 (tpp) cc_final: 0.7856 (tpp) REVERT: C 717 MET cc_start: 0.7588 (mpp) cc_final: 0.7138 (mtt) REVERT: D 304 VAL cc_start: 0.9515 (t) cc_final: 0.9276 (p) REVERT: D 414 ASP cc_start: 0.7737 (m-30) cc_final: 0.7271 (t0) REVERT: D 440 MET cc_start: 0.8627 (mtt) cc_final: 0.8285 (mmt) REVERT: D 555 MET cc_start: 0.8399 (tmm) cc_final: 0.8108 (tmm) REVERT: D 706 MET cc_start: 0.8546 (tpp) cc_final: 0.7909 (tpp) REVERT: D 717 MET cc_start: 0.7574 (mpp) cc_final: 0.7124 (mtt) outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.1317 time to fit residues: 107.5027 Evaluate side-chains 381 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 177 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A 452 ASN B 220 ASN B 339 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN D 339 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094141 restraints weight = 56145.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096664 restraints weight = 32220.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098398 restraints weight = 21749.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099562 restraints weight = 16367.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100392 restraints weight = 13414.266| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21432 Z= 0.148 Angle : 0.749 7.790 28948 Z= 0.372 Chirality : 0.044 0.220 3292 Planarity : 0.005 0.074 3600 Dihedral : 7.094 47.593 2836 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.36 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.96 (0.17), residues: 2556 helix: -0.06 (0.14), residues: 1380 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 363 TYR 0.017 0.002 TYR C 594 PHE 0.027 0.002 PHE C 538 TRP 0.008 0.001 TRP C 521 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (21420) covalent geometry : angle 0.74913 / 0.37 (28948) hydrogen bonds : bond 0.02983 / 1.97 ( 696) hydrogen bonds : angle 4.17640 / 2.94 ( 2028) Misc. bond : bond 0.00143 / 0.08 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8442 (mttt) cc_final: 0.7632 (tmtt) REVERT: A 347 LEU cc_start: 0.9013 (tt) cc_final: 0.8739 (tt) REVERT: A 414 ASP cc_start: 0.7456 (m-30) cc_final: 0.7221 (t0) REVERT: A 440 MET cc_start: 0.8618 (mtt) cc_final: 0.8327 (mmp) REVERT: A 555 MET cc_start: 0.8642 (tmm) cc_final: 0.8279 (tmm) REVERT: A 578 MET cc_start: 0.8556 (tpp) cc_final: 0.8274 (tpp) REVERT: A 594 TYR cc_start: 0.9149 (t80) cc_final: 0.8806 (t80) REVERT: A 706 MET cc_start: 0.8546 (tpp) cc_final: 0.7903 (tpp) REVERT: A 717 MET cc_start: 0.7593 (mpp) cc_final: 0.7110 (mtt) REVERT: B 293 ASP cc_start: 0.7987 (m-30) cc_final: 0.7668 (m-30) REVERT: B 321 TYR cc_start: 0.9017 (t80) cc_final: 0.8759 (t80) REVERT: B 405 GLU cc_start: 0.8755 (pt0) cc_final: 0.8453 (pt0) REVERT: B 414 ASP cc_start: 0.7726 (m-30) cc_final: 0.7300 (t0) REVERT: B 440 MET cc_start: 0.8646 (mtt) cc_final: 0.8259 (mmp) REVERT: B 555 MET cc_start: 0.8463 (tmm) cc_final: 0.8057 (tmm) REVERT: B 594 TYR cc_start: 0.9163 (t80) cc_final: 0.8948 (t80) REVERT: B 672 MET cc_start: 0.8794 (tpp) cc_final: 0.8447 (tpt) REVERT: B 706 MET cc_start: 0.8558 (tpp) cc_final: 0.7932 (tpp) REVERT: B 717 MET cc_start: 0.7540 (mpp) cc_final: 0.7085 (mtt) REVERT: C 300 LEU cc_start: 0.9606 (mp) cc_final: 0.9391 (mt) REVERT: C 405 GLU cc_start: 0.8747 (pt0) cc_final: 0.8441 (pt0) REVERT: C 414 ASP cc_start: 0.7705 (m-30) cc_final: 0.7283 (t0) REVERT: C 440 MET cc_start: 0.8621 (mtt) cc_final: 0.8250 (mmp) REVERT: C 521 TRP cc_start: 0.8769 (t60) cc_final: 0.8296 (t60) REVERT: C 555 MET cc_start: 0.8501 (tmm) cc_final: 0.8073 (tmm) REVERT: C 580 GLN cc_start: 0.8754 (tp40) cc_final: 0.8358 (tp40) REVERT: C 706 MET cc_start: 0.8525 (tpp) cc_final: 0.7906 (tpp) REVERT: C 717 MET cc_start: 0.7585 (mpp) cc_final: 0.7069 (mtt) REVERT: D 356 ILE cc_start: 0.9371 (tp) cc_final: 0.9051 (tp) REVERT: D 440 MET cc_start: 0.8618 (mtt) cc_final: 0.8228 (mmp) REVERT: D 555 MET cc_start: 0.8520 (tmm) cc_final: 0.8095 (tmm) REVERT: D 574 MET cc_start: 0.8792 (ppp) cc_final: 0.7572 (ptt) REVERT: D 578 MET cc_start: 0.7842 (mtm) cc_final: 0.7307 (mtm) REVERT: D 677 MET cc_start: 0.8870 (mmm) cc_final: 0.8517 (mmm) REVERT: D 704 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8424 (tm-30) REVERT: D 717 MET cc_start: 0.7608 (mpp) cc_final: 0.7083 (mtt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1309 time to fit residues: 105.0165 Evaluate side-chains 402 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 244 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 233 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 346 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096340 restraints weight = 55556.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098839 restraints weight = 32073.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100556 restraints weight = 21692.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101771 restraints weight = 16365.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102610 restraints weight = 13341.279| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21432 Z= 0.130 Angle : 0.735 7.931 28948 Z= 0.367 Chirality : 0.043 0.220 3292 Planarity : 0.005 0.073 3600 Dihedral : 6.953 47.558 2836 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.48 % Favored : 85.37 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.86 (0.17), residues: 2556 helix: 0.14 (0.14), residues: 1352 sheet: -4.11 (0.68), residues: 52 loop : -2.89 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 363 TYR 0.013 0.001 TYR A 594 PHE 0.026 0.001 PHE A 538 TRP 0.010 0.001 TRP C 710 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (21420) covalent geometry : angle 0.73513 / 0.37 (28948) hydrogen bonds : bond 0.02857 / 1.88 ( 696) hydrogen bonds : angle 4.09296 / 2.90 ( 2028) Misc. bond : bond 0.00149 / 0.08 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.30 seconds wall clock time: 58 minutes 54.40 seconds (3534.40 seconds total)