Starting phenix.real_space_refine on Wed Nov 19 04:52:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_8921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_8921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_8921.map" model { file = "/net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_8921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dvz_8921/11_2025/6dvz_8921.cif" } 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-2.0-5881/lib/python3.9/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: 5.19, per 1000 atoms: 0.25 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: 1.85 Conformation dependent library (CDL) restraints added in 773.4 milliseconds 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: 0.69 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: 3.24 Time building geometry restraints manager: 2.46 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: 12300 23.85 - 47.71: 412 47.71 - 71.56: 32 71.56 - 95.42: 20 95.42 - 119.27: 4 Dihedral angle restraints: 12768 sinusoidal: 5184 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 12765 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.940 Find NCS groups from input model: 0.150 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 12.685 119.270 7840 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 covalent geometry : bond 0.00844 (21420) covalent geometry : angle 1.27023 (28948) hydrogen bonds : bond 0.31227 ( 696) hydrogen bonds : angle 10.52292 ( 2028) Misc. bond : bond 0.00585 ( 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 : 0.848 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: 0.8019 (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: 0.8426 (t80) REVERT: A 414 ASP cc_start: 0.7582 (m-30) cc_final: 0.6947 (t0) REVERT: A 440 MET cc_start: 0.8537 (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: 0.9041 (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: 0.8380 (m-30) cc_final: 0.7943 (t0) REVERT: B 321 TYR cc_start: 0.8694 (t80) cc_final: 0.8436 (t80) REVERT: B 414 ASP cc_start: 0.7551 (m-30) cc_final: 0.6911 (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: 0.7004 (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: 0.8014 (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: 0.8686 (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: 0.8886 (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: 0.8505 (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: 0.1503 time to fit residues: 164.5997 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 : 0.802 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3611 r_free = 0.3611 target = 0.112655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094871 restraints weight = 56728.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097386 restraints weight = 31444.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099077 restraints weight = 20853.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100215 restraints weight = 15630.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100952 restraints weight = 12786.875| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3119 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= 0.154 Angle : 0.787 9.098 28948 Z= 0.406 Chirality : 0.044 0.220 3292 Planarity : 0.006 0.068 3600 Dihedral : 9.729 99.112 2860 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.75 % Favored : 85.09 % 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: -4.12 (0.68), residues: 52 loop : -3.63 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 714 TYR 0.020 0.002 TYR A 540 PHE 0.020 0.002 PHE A 538 TRP 0.011 0.001 TRP D 481 HIS 0.007 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00330 (21420) covalent geometry : angle 0.78722 (28948) hydrogen bonds : bond 0.05262 ( 696) hydrogen bonds : angle 5.24867 ( 2028) Misc. bond : bond 0.00156 ( 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 : 0.843 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: A 150 ARG cc_start: 0.7896 (pmt-80) cc_final: 0.7393 (ptp-170) REVERT: A 298 ASN cc_start: 0.9320 (p0) cc_final: 0.9038 (p0) REVERT: A 309 ASP cc_start: 0.8251 (m-30) cc_final: 0.7796 (t0) REVERT: A 321 TYR cc_start: 0.8621 (t80) cc_final: 0.8363 (t80) REVERT: A 440 MET cc_start: 0.8803 (mtt) cc_final: 0.8311 (mmp) REVERT: A 663 ILE cc_start: 0.9732 (tp) cc_final: 0.9532 (tp) REVERT: A 670 LEU cc_start: 0.9595 (mm) cc_final: 0.9274 (tp) REVERT: A 679 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 150 ARG cc_start: 0.7899 (pmt-80) cc_final: 0.7400 (ptp-170) REVERT: B 298 ASN cc_start: 0.9316 (p0) cc_final: 0.9045 (p0) REVERT: B 309 ASP cc_start: 0.8227 (m-30) cc_final: 0.7794 (t0) REVERT: B 321 TYR cc_start: 0.8644 (t80) cc_final: 0.8392 (t80) REVERT: B 440 MET cc_start: 0.8795 (mtt) cc_final: 0.8302 (mmp) REVERT: B 538 PHE cc_start: 0.7294 (t80) cc_final: 0.7063 (t80) REVERT: B 663 ILE cc_start: 0.9739 (tp) cc_final: 0.9537 (tp) REVERT: B 670 LEU cc_start: 0.9608 (mm) cc_final: 0.9284 (tp) REVERT: C 150 ARG cc_start: 0.7905 (pmt-80) cc_final: 0.7400 (ptp-170) REVERT: C 298 ASN cc_start: 0.9311 (p0) cc_final: 0.9066 (p0) REVERT: C 309 ASP cc_start: 0.8228 (m-30) cc_final: 0.7798 (t0) REVERT: C 321 TYR cc_start: 0.8633 (t80) cc_final: 0.8371 (t80) REVERT: C 347 LEU cc_start: 0.9570 (tp) cc_final: 0.9365 (tt) REVERT: C 440 MET cc_start: 0.8801 (mtt) cc_final: 0.8299 (mmp) REVERT: C 538 PHE cc_start: 0.7294 (t80) cc_final: 0.7062 (t80) REVERT: C 663 ILE cc_start: 0.9735 (tp) cc_final: 0.9530 (tp) REVERT: C 670 LEU cc_start: 0.9595 (mm) cc_final: 0.9276 (tp) REVERT: C 679 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 150 ARG cc_start: 0.7890 (pmt-80) cc_final: 0.7392 (ptp-170) REVERT: D 298 ASN cc_start: 0.9320 (p0) cc_final: 0.9036 (p0) REVERT: D 309 ASP cc_start: 0.8245 (m-30) cc_final: 0.7792 (t0) REVERT: D 321 TYR cc_start: 0.8612 (t80) cc_final: 0.8356 (t80) REVERT: D 440 MET cc_start: 0.8797 (mtt) cc_final: 0.8304 (mmp) REVERT: D 538 PHE cc_start: 0.7286 (t80) cc_final: 0.7062 (t80) REVERT: D 663 ILE cc_start: 0.9730 (tp) cc_final: 0.9528 (tp) REVERT: D 670 LEU cc_start: 0.9576 (mm) cc_final: 0.9304 (tp) outliers start: 2 outliers final: 0 residues processed: 618 average time/residue: 0.1417 time to fit residues: 138.9605 Evaluate side-chains 439 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 0.7980 chunk 215 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3642 r_free = 0.3642 target = 0.114295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096302 restraints weight = 55959.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098897 restraints weight = 31525.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100613 restraints weight = 21003.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101842 restraints weight = 15785.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102580 restraints weight = 12867.103| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21432 Z= 0.141 Angle : 0.705 7.977 28948 Z= 0.366 Chirality : 0.043 0.225 3292 Planarity : 0.005 0.070 3600 Dihedral : 8.846 76.656 2860 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.73 % Favored : 84.12 % Rotamer: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % 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: -3.40 (0.15), residues: 2556 helix: -1.31 (0.13), residues: 1368 sheet: -3.78 (0.74), residues: 52 loop : -3.43 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.017 0.002 TYR C 540 PHE 0.018 0.001 PHE C 259 TRP 0.011 0.001 TRP D 521 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00314 (21420) covalent geometry : angle 0.70532 (28948) hydrogen bonds : bond 0.03816 ( 696) hydrogen bonds : angle 4.47457 ( 2028) Misc. bond : bond 0.00151 ( 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 584 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 582 time to evaluate : 0.872 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: A 150 ARG cc_start: 0.7932 (pmt-80) cc_final: 0.7418 (ptp-170) REVERT: A 224 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7969 (tp30) REVERT: A 309 ASP cc_start: 0.8263 (m-30) cc_final: 0.7837 (t0) REVERT: A 311 LYS cc_start: 0.8532 (mttt) cc_final: 0.7456 (tmtt) REVERT: A 321 TYR cc_start: 0.8752 (t80) cc_final: 0.8526 (t80) REVERT: A 440 MET cc_start: 0.8646 (mtt) cc_final: 0.8238 (mmp) REVERT: A 538 PHE cc_start: 0.7302 (t80) cc_final: 0.7074 (t80) REVERT: A 717 MET cc_start: 0.7362 (mpp) cc_final: 0.7084 (mtt) REVERT: B 150 ARG cc_start: 0.7917 (pmt-80) cc_final: 0.7420 (ptp-170) REVERT: B 224 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7970 (tp30) REVERT: B 309 ASP cc_start: 0.8265 (m-30) cc_final: 0.7844 (t0) REVERT: B 311 LYS cc_start: 0.8533 (mttt) cc_final: 0.7468 (tmtt) REVERT: B 440 MET cc_start: 0.8626 (mtt) cc_final: 0.8227 (mmp) REVERT: B 717 MET cc_start: 0.7359 (mpp) cc_final: 0.7086 (mtt) REVERT: C 150 ARG cc_start: 0.7928 (pmt-80) cc_final: 0.7423 (ptp-170) REVERT: C 224 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7964 (tp30) REVERT: C 309 ASP cc_start: 0.8259 (m-30) cc_final: 0.7825 (t0) REVERT: C 311 LYS cc_start: 0.8529 (mttt) cc_final: 0.7467 (tmtt) REVERT: C 321 TYR cc_start: 0.8755 (t80) cc_final: 0.8552 (t80) REVERT: C 414 ASP cc_start: 0.7489 (m-30) cc_final: 0.6807 (t0) REVERT: C 440 MET cc_start: 0.8620 (mtt) cc_final: 0.8205 (mmp) REVERT: C 717 MET cc_start: 0.7387 (mpp) cc_final: 0.7111 (mtt) REVERT: D 150 ARG cc_start: 0.7914 (pmt-80) cc_final: 0.7421 (ptp-170) REVERT: D 224 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7969 (tp30) REVERT: D 309 ASP cc_start: 0.8256 (m-30) cc_final: 0.7829 (t0) REVERT: D 311 LYS cc_start: 0.8525 (mttt) cc_final: 0.7458 (tmtt) REVERT: D 321 TYR cc_start: 0.8759 (t80) cc_final: 0.8533 (t80) REVERT: D 440 MET cc_start: 0.8614 (mtt) cc_final: 0.8215 (mmp) REVERT: D 717 MET cc_start: 0.7380 (mpp) cc_final: 0.7096 (mtt) outliers start: 2 outliers final: 0 residues processed: 584 average time/residue: 0.1311 time to fit residues: 124.2656 Evaluate side-chains 395 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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: 4.9990 chunk 143 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 251 optimal weight: 0.0170 chunk 30 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 339 ASN ** 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 339 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 178 ASN D 339 ASN D 645 GLN D 671 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092472 restraints weight = 56824.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094912 restraints weight = 32443.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096562 restraints weight = 21938.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097680 restraints weight = 16652.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098498 restraints weight = 13654.675| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21432 Z= 0.212 Angle : 0.754 7.838 28948 Z= 0.389 Chirality : 0.045 0.227 3292 Planarity : 0.005 0.070 3600 Dihedral : 8.727 65.592 2860 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.59 % Favored : 83.26 % Rotamer: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % 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: -3.00 (0.16), residues: 2556 helix: -0.87 (0.13), residues: 1376 sheet: None (None), residues: 0 loop : -3.48 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.021 0.002 TYR C 451 PHE 0.024 0.002 PHE A 654 TRP 0.007 0.001 TRP C 739 HIS 0.008 0.002 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00476 (21420) covalent geometry : angle 0.75386 (28948) hydrogen bonds : bond 0.03748 ( 696) hydrogen bonds : angle 4.51840 ( 2028) Misc. bond : bond 0.00120 ( 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 525 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 0.836 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 150 ARG cc_start: 0.7593 (pmt-80) cc_final: 0.7302 (ptp-170) REVERT: A 309 ASP cc_start: 0.8222 (m-30) cc_final: 0.7864 (t0) REVERT: A 414 ASP cc_start: 0.7649 (m-30) cc_final: 0.6906 (t0) REVERT: A 440 MET cc_start: 0.8704 (mtt) cc_final: 0.8280 (mmt) REVERT: A 555 MET cc_start: 0.8416 (tmm) cc_final: 0.7968 (tmm) REVERT: A 594 TYR cc_start: 0.9167 (t80) cc_final: 0.8726 (t80) REVERT: A 598 LEU cc_start: 0.9102 (tt) cc_final: 0.8858 (tt) REVERT: A 727 ASP cc_start: 0.7329 (p0) cc_final: 0.6912 (p0) REVERT: B 150 ARG cc_start: 0.7583 (pmt-80) cc_final: 0.7308 (ptp-170) REVERT: B 309 ASP cc_start: 0.8204 (m-30) cc_final: 0.7864 (t0) REVERT: B 414 ASP cc_start: 0.7639 (m-30) cc_final: 0.6906 (t0) REVERT: B 440 MET cc_start: 0.8668 (mtt) cc_final: 0.8259 (mmt) REVERT: B 538 PHE cc_start: 0.7430 (t80) cc_final: 0.7153 (t80) REVERT: B 594 TYR cc_start: 0.9156 (t80) cc_final: 0.8698 (t80) REVERT: B 598 LEU cc_start: 0.9098 (tt) cc_final: 0.8855 (tt) REVERT: C 150 ARG cc_start: 0.7596 (pmt-80) cc_final: 0.7311 (ptp-170) REVERT: C 309 ASP cc_start: 0.8203 (m-30) cc_final: 0.7865 (t0) REVERT: C 414 ASP cc_start: 0.7625 (m-30) cc_final: 0.6886 (t0) REVERT: C 440 MET cc_start: 0.8660 (mtt) cc_final: 0.8253 (mmt) REVERT: C 538 PHE cc_start: 0.7444 (t80) cc_final: 0.7175 (t80) REVERT: C 594 TYR cc_start: 0.9148 (t80) cc_final: 0.8710 (t80) REVERT: C 598 LEU cc_start: 0.9092 (tt) cc_final: 0.8850 (tt) REVERT: D 150 ARG cc_start: 0.7604 (pmt-80) cc_final: 0.7319 (ptp-170) REVERT: D 309 ASP cc_start: 0.8229 (m-30) cc_final: 0.7871 (t0) REVERT: D 414 ASP cc_start: 0.7636 (m-30) cc_final: 0.6898 (t0) REVERT: D 440 MET cc_start: 0.8710 (mtt) cc_final: 0.8266 (mmt) REVERT: D 538 PHE cc_start: 0.7429 (t80) cc_final: 0.7167 (t80) REVERT: D 594 TYR cc_start: 0.9156 (t80) cc_final: 0.8719 (t80) REVERT: D 598 LEU cc_start: 0.9141 (tt) cc_final: 0.8914 (tt) REVERT: D 679 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8135 (tm-30) REVERT: D 727 ASP cc_start: 0.7309 (p0) cc_final: 0.6855 (p0) outliers start: 3 outliers final: 0 residues processed: 525 average time/residue: 0.1304 time to fit residues: 111.5176 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 : 0.830 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 30.0000 chunk 164 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 645 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 = 0.113901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095850 restraints weight = 55656.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098457 restraints weight = 31191.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100186 restraints weight = 20705.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101309 restraints weight = 15483.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102204 restraints weight = 12684.715| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21432 Z= 0.133 Angle : 0.704 9.469 28948 Z= 0.360 Chirality : 0.043 0.225 3292 Planarity : 0.005 0.070 3600 Dihedral : 8.138 55.459 2860 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.79 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -2.65 (0.16), residues: 2556 helix: -0.60 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -3.32 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.017 0.001 TYR A 540 PHE 0.019 0.001 PHE A 654 TRP 0.007 0.001 TRP D 710 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00301 (21420) covalent geometry : angle 0.70405 (28948) hydrogen bonds : bond 0.03219 ( 696) hydrogen bonds : angle 4.21757 ( 2028) Misc. bond : bond 0.00214 ( 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 547 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 0.852 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: A 150 ARG cc_start: 0.7670 (pmt-80) cc_final: 0.7371 (ptp-170) REVERT: A 224 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 309 ASP cc_start: 0.8202 (m-30) cc_final: 0.7844 (t0) REVERT: A 414 ASP cc_start: 0.7611 (m-30) cc_final: 0.6933 (t0) REVERT: A 440 MET cc_start: 0.8591 (mtt) cc_final: 0.8228 (mmt) REVERT: A 538 PHE cc_start: 0.7430 (t80) cc_final: 0.7229 (t80) REVERT: A 555 MET cc_start: 0.8545 (tmm) cc_final: 0.8029 (tmm) REVERT: A 717 MET cc_start: 0.7395 (mpp) cc_final: 0.6963 (mtt) REVERT: B 129 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 148 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7739 (mmm160) REVERT: B 224 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 309 ASP cc_start: 0.8196 (m-30) cc_final: 0.7863 (t0) REVERT: B 414 ASP cc_start: 0.7612 (m-30) cc_final: 0.6940 (t0) REVERT: B 440 MET cc_start: 0.8594 (mtt) cc_final: 0.8205 (mmt) REVERT: B 538 PHE cc_start: 0.7368 (t80) cc_final: 0.7129 (t80) REVERT: B 717 MET cc_start: 0.7510 (mpp) cc_final: 0.7027 (mtt) REVERT: C 150 ARG cc_start: 0.7667 (pmt-80) cc_final: 0.7376 (ptp-170) REVERT: C 224 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 298 ASN cc_start: 0.9155 (p0) cc_final: 0.8916 (p0) REVERT: C 309 ASP cc_start: 0.8200 (m-30) cc_final: 0.7851 (t0) REVERT: C 414 ASP cc_start: 0.7594 (m-30) cc_final: 0.6924 (t0) REVERT: C 440 MET cc_start: 0.8606 (mtt) cc_final: 0.8211 (mmt) REVERT: C 538 PHE cc_start: 0.7375 (t80) cc_final: 0.7145 (t80) REVERT: C 717 MET cc_start: 0.7543 (mpp) cc_final: 0.7048 (mtt) REVERT: D 150 ARG cc_start: 0.7662 (pmt-80) cc_final: 0.7384 (ptp-170) REVERT: D 224 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 309 ASP cc_start: 0.8208 (m-30) cc_final: 0.7831 (t0) REVERT: D 414 ASP cc_start: 0.7604 (m-30) cc_final: 0.6920 (t0) REVERT: D 440 MET cc_start: 0.8592 (mtt) cc_final: 0.8235 (mmt) REVERT: D 538 PHE cc_start: 0.7367 (t80) cc_final: 0.7134 (t80) REVERT: D 717 MET cc_start: 0.7429 (mpp) cc_final: 0.6995 (mtt) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.1328 time to fit residues: 118.5700 Evaluate side-chains 396 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 4.9990 chunk 219 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 645 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 = 0.3634 r_free = 0.3634 target = 0.113243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095054 restraints weight = 55671.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097635 restraints weight = 31930.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099388 restraints weight = 21479.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100604 restraints weight = 16139.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101404 restraints weight = 13171.444| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21432 Z= 0.142 Angle : 0.721 10.668 28948 Z= 0.365 Chirality : 0.043 0.222 3292 Planarity : 0.005 0.071 3600 Dihedral : 7.884 57.104 2860 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.65 % Favored : 84.19 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -2.33 (0.17), residues: 2556 helix: -0.33 (0.14), residues: 1372 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 226 TYR 0.022 0.001 TYR A 451 PHE 0.020 0.001 PHE D 654 TRP 0.020 0.001 TRP A 521 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00327 (21420) covalent geometry : angle 0.72074 (28948) hydrogen bonds : bond 0.03078 ( 696) hydrogen bonds : angle 4.18425 ( 2028) Misc. bond : bond 0.00173 ( 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 532 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.889 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: A 148 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7743 (mmm160) REVERT: A 304 VAL cc_start: 0.9515 (t) cc_final: 0.9281 (p) REVERT: A 309 ASP cc_start: 0.8195 (m-30) cc_final: 0.7862 (t0) REVERT: A 414 ASP cc_start: 0.7404 (m-30) cc_final: 0.6967 (t0) REVERT: A 440 MET cc_start: 0.8566 (mtt) cc_final: 0.8227 (mmt) REVERT: A 521 TRP cc_start: 0.8654 (t60) cc_final: 0.7941 (t60) REVERT: A 538 PHE cc_start: 0.7472 (t80) cc_final: 0.7232 (t80) REVERT: A 574 MET cc_start: 0.9071 (ppp) cc_final: 0.8672 (ppp) REVERT: A 717 MET cc_start: 0.7465 (mpp) cc_final: 0.7083 (mtt) REVERT: B 148 ARG cc_start: 0.8101 (mmt90) cc_final: 0.7728 (mmm160) REVERT: B 303 LEU cc_start: 0.9163 (mp) cc_final: 0.8945 (mp) REVERT: B 309 ASP cc_start: 0.8226 (m-30) cc_final: 0.7899 (t0) REVERT: B 321 TYR cc_start: 0.8724 (t80) cc_final: 0.8517 (t80) REVERT: B 414 ASP cc_start: 0.7404 (m-30) cc_final: 0.7016 (t0) REVERT: B 440 MET cc_start: 0.8591 (mtt) cc_final: 0.8222 (mmt) REVERT: B 521 TRP cc_start: 0.8645 (t60) cc_final: 0.7934 (t60) REVERT: B 555 MET cc_start: 0.8437 (tmm) cc_final: 0.8081 (tmm) REVERT: B 594 TYR cc_start: 0.9132 (t80) cc_final: 0.8925 (t80) REVERT: B 672 MET cc_start: 0.8692 (tpp) cc_final: 0.8441 (tpt) REVERT: B 717 MET cc_start: 0.7440 (mpp) cc_final: 0.7097 (mtt) REVERT: C 148 ARG cc_start: 0.8161 (mmt90) cc_final: 0.7753 (mmm160) REVERT: C 304 VAL cc_start: 0.9530 (t) cc_final: 0.9277 (p) REVERT: C 309 ASP cc_start: 0.8213 (m-30) cc_final: 0.7876 (t0) REVERT: C 414 ASP cc_start: 0.7390 (m-30) cc_final: 0.7006 (t0) REVERT: C 440 MET cc_start: 0.8581 (mtt) cc_final: 0.8215 (mmt) REVERT: C 555 MET cc_start: 0.8436 (tmm) cc_final: 0.8097 (tmm) REVERT: C 574 MET cc_start: 0.8144 (ttp) cc_final: 0.7540 (ptp) REVERT: C 717 MET cc_start: 0.7452 (mpp) cc_final: 0.7105 (mtt) REVERT: D 148 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7759 (mmm160) REVERT: D 304 VAL cc_start: 0.9520 (t) cc_final: 0.9298 (p) REVERT: D 309 ASP cc_start: 0.8208 (m-30) cc_final: 0.7860 (t0) REVERT: D 321 TYR cc_start: 0.8867 (t80) cc_final: 0.8648 (t80) REVERT: D 414 ASP cc_start: 0.7506 (m-30) cc_final: 0.6989 (t0) REVERT: D 440 MET cc_start: 0.8561 (mtt) cc_final: 0.8220 (mmt) REVERT: D 521 TRP cc_start: 0.8640 (t60) cc_final: 0.7955 (t60) REVERT: D 555 MET cc_start: 0.8430 (tmm) cc_final: 0.8067 (tmm) REVERT: D 717 MET cc_start: 0.7459 (mpp) cc_final: 0.7087 (mtt) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1352 time to fit residues: 115.9036 Evaluate side-chains 390 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 251 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 227 optimal weight: 30.0000 chunk 206 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 220 ASN C 339 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094598 restraints weight = 56086.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097147 restraints weight = 32138.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098870 restraints weight = 21649.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100060 restraints weight = 16307.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100870 restraints weight = 13352.838| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4838 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= 0.151 Angle : 0.746 8.958 28948 Z= 0.373 Chirality : 0.043 0.225 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.803 58.358 2860 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.41 % Favored : 84.43 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -2.28 (0.17), residues: 2556 helix: -0.24 (0.14), residues: 1384 sheet: -4.03 (0.68), residues: 52 loop : -3.13 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.022 0.002 TYR B 451 PHE 0.028 0.002 PHE C 522 TRP 0.010 0.001 TRP C 521 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00344 (21420) covalent geometry : angle 0.74641 (28948) hydrogen bonds : bond 0.03160 ( 696) hydrogen bonds : angle 4.16869 ( 2028) Misc. bond : bond 0.00144 ( 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 508 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.872 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: A 148 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7704 (mmm160) REVERT: A 309 ASP cc_start: 0.8224 (m-30) cc_final: 0.7917 (t0) REVERT: A 321 TYR cc_start: 0.8950 (t80) cc_final: 0.8690 (t80) REVERT: A 347 LEU cc_start: 0.9327 (tp) cc_final: 0.8988 (tt) REVERT: A 405 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 414 ASP cc_start: 0.7474 (m-30) cc_final: 0.7012 (t0) REVERT: A 440 MET cc_start: 0.8590 (mtt) cc_final: 0.8240 (mmt) REVERT: A 521 TRP cc_start: 0.8903 (t60) cc_final: 0.8069 (t60) REVERT: A 555 MET cc_start: 0.8470 (tmm) cc_final: 0.8187 (tmm) REVERT: A 574 MET cc_start: 0.8887 (ppp) cc_final: 0.8662 (ppp) REVERT: A 594 TYR cc_start: 0.9210 (t80) cc_final: 0.8949 (t80) REVERT: A 704 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 717 MET cc_start: 0.7488 (mpp) cc_final: 0.7118 (mtt) REVERT: B 148 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7618 (mmm160) REVERT: B 304 VAL cc_start: 0.9556 (t) cc_final: 0.9317 (p) REVERT: B 309 ASP cc_start: 0.8241 (m-30) cc_final: 0.7917 (t0) REVERT: B 406 ILE cc_start: 0.9593 (tp) cc_final: 0.9387 (mm) REVERT: B 414 ASP cc_start: 0.7496 (m-30) cc_final: 0.6991 (t0) REVERT: B 440 MET cc_start: 0.8619 (mtt) cc_final: 0.8266 (mmt) REVERT: B 521 TRP cc_start: 0.8858 (t60) cc_final: 0.8061 (t60) REVERT: B 555 MET cc_start: 0.8433 (tmm) cc_final: 0.7981 (tmm) REVERT: B 704 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 717 MET cc_start: 0.7492 (mpp) cc_final: 0.6934 (mtt) REVERT: C 148 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7694 (mmm160) REVERT: C 309 ASP cc_start: 0.8240 (m-30) cc_final: 0.7930 (t0) REVERT: C 321 TYR cc_start: 0.8858 (t80) cc_final: 0.8638 (t80) REVERT: C 406 ILE cc_start: 0.9590 (tp) cc_final: 0.9378 (mm) REVERT: C 414 ASP cc_start: 0.7467 (m-30) cc_final: 0.6990 (t0) REVERT: C 440 MET cc_start: 0.8589 (mtt) cc_final: 0.8238 (mmt) REVERT: C 555 MET cc_start: 0.8451 (tmm) cc_final: 0.7961 (tmm) REVERT: C 677 MET cc_start: 0.8751 (mmm) cc_final: 0.8511 (mmm) REVERT: C 704 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8240 (tm-30) REVERT: C 717 MET cc_start: 0.7496 (mpp) cc_final: 0.6934 (mtt) REVERT: D 148 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7659 (mmm160) REVERT: D 304 VAL cc_start: 0.9514 (t) cc_final: 0.9258 (p) REVERT: D 309 ASP cc_start: 0.8243 (m-30) cc_final: 0.7919 (t0) REVERT: D 321 TYR cc_start: 0.8884 (t80) cc_final: 0.8580 (t80) REVERT: D 347 LEU cc_start: 0.9327 (tp) cc_final: 0.8975 (tt) REVERT: D 405 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8102 (mt-10) REVERT: D 414 ASP cc_start: 0.7603 (m-30) cc_final: 0.6996 (t0) REVERT: D 440 MET cc_start: 0.8587 (mtt) cc_final: 0.8240 (mmt) REVERT: D 521 TRP cc_start: 0.8889 (t60) cc_final: 0.8090 (t60) REVERT: D 555 MET cc_start: 0.8425 (tmm) cc_final: 0.7971 (tmm) REVERT: D 594 TYR cc_start: 0.9184 (t80) cc_final: 0.8982 (t80) REVERT: D 717 MET cc_start: 0.7445 (mpp) cc_final: 0.7133 (mtt) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.1335 time to fit residues: 109.8004 Evaluate side-chains 371 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 9.9990 chunk 79 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 220 ASN B 339 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN D 220 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096305 restraints weight = 55550.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098951 restraints weight = 30897.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100756 restraints weight = 20327.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101979 restraints weight = 15051.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102803 restraints weight = 12137.817| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21432 Z= 0.128 Angle : 0.724 8.317 28948 Z= 0.361 Chirality : 0.043 0.222 3292 Planarity : 0.005 0.072 3600 Dihedral : 7.664 58.252 2860 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.59 % Favored : 85.25 % 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 : 0.00 % 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: -2.14 (0.17), residues: 2556 helix: -0.16 (0.14), residues: 1388 sheet: -4.00 (0.67), residues: 52 loop : -3.00 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.013 0.001 TYR C 540 PHE 0.025 0.001 PHE B 538 TRP 0.013 0.001 TRP B 521 HIS 0.005 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00288 (21420) covalent geometry : angle 0.72357 (28948) hydrogen bonds : bond 0.02956 ( 696) hydrogen bonds : angle 4.09463 ( 2028) Misc. bond : bond 0.00141 ( 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 513 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 0.861 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 148 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7628 (mmm160) REVERT: A 304 VAL cc_start: 0.9482 (t) cc_final: 0.9223 (p) REVERT: A 309 ASP cc_start: 0.8190 (m-30) cc_final: 0.7911 (t0) REVERT: A 311 LYS cc_start: 0.8442 (mttt) cc_final: 0.7623 (tmtt) REVERT: A 321 TYR cc_start: 0.8858 (t80) cc_final: 0.8533 (t80) REVERT: A 405 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 414 ASP cc_start: 0.7343 (m-30) cc_final: 0.6966 (t0) REVERT: A 440 MET cc_start: 0.8641 (mtt) cc_final: 0.8300 (mmt) REVERT: A 521 TRP cc_start: 0.8903 (t60) cc_final: 0.8130 (t60) REVERT: A 555 MET cc_start: 0.8485 (tmm) cc_final: 0.8163 (tmm) REVERT: A 594 TYR cc_start: 0.9114 (t80) cc_final: 0.8902 (t80) REVERT: A 717 MET cc_start: 0.7466 (mpp) cc_final: 0.7059 (mtt) REVERT: B 148 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7697 (mmm160) REVERT: B 304 VAL cc_start: 0.9518 (t) cc_final: 0.9296 (p) REVERT: B 309 ASP cc_start: 0.8225 (m-30) cc_final: 0.7920 (t0) REVERT: B 311 LYS cc_start: 0.8419 (mttt) cc_final: 0.7636 (tmtt) REVERT: B 414 ASP cc_start: 0.7312 (m-30) cc_final: 0.6975 (t0) REVERT: B 440 MET cc_start: 0.8646 (mtt) cc_final: 0.8255 (mmp) REVERT: B 521 TRP cc_start: 0.8914 (t60) cc_final: 0.8122 (t60) REVERT: B 555 MET cc_start: 0.8499 (tmm) cc_final: 0.7916 (tmm) REVERT: B 594 TYR cc_start: 0.9192 (t80) cc_final: 0.8948 (t80) REVERT: B 706 MET cc_start: 0.8474 (tpp) cc_final: 0.7751 (tpp) REVERT: B 717 MET cc_start: 0.7463 (mpp) cc_final: 0.7037 (mtt) REVERT: C 309 ASP cc_start: 0.8224 (m-30) cc_final: 0.7936 (t0) REVERT: C 311 LYS cc_start: 0.8439 (mttt) cc_final: 0.7614 (tmtt) REVERT: C 321 TYR cc_start: 0.8798 (t80) cc_final: 0.8557 (t80) REVERT: C 414 ASP cc_start: 0.7306 (m-30) cc_final: 0.6966 (t0) REVERT: C 440 MET cc_start: 0.8642 (mtt) cc_final: 0.8255 (mmp) REVERT: C 555 MET cc_start: 0.8495 (tmm) cc_final: 0.7893 (tmm) REVERT: C 706 MET cc_start: 0.8472 (tpp) cc_final: 0.7753 (tpp) REVERT: C 717 MET cc_start: 0.7480 (mpp) cc_final: 0.7055 (mtt) REVERT: D 148 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7626 (mmm160) REVERT: D 224 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 304 VAL cc_start: 0.9476 (t) cc_final: 0.9230 (p) REVERT: D 309 ASP cc_start: 0.8210 (m-30) cc_final: 0.7919 (t0) REVERT: D 311 LYS cc_start: 0.8448 (mttt) cc_final: 0.7627 (tmtt) REVERT: D 321 TYR cc_start: 0.8850 (t80) cc_final: 0.8573 (t80) REVERT: D 347 LEU cc_start: 0.9288 (tp) cc_final: 0.8988 (tt) REVERT: D 405 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 414 ASP cc_start: 0.7392 (m-30) cc_final: 0.6992 (t0) REVERT: D 440 MET cc_start: 0.8642 (mtt) cc_final: 0.8234 (mmp) REVERT: D 521 TRP cc_start: 0.8925 (t60) cc_final: 0.8145 (t60) REVERT: D 555 MET cc_start: 0.8472 (tmm) cc_final: 0.7919 (tmm) REVERT: D 594 TYR cc_start: 0.9187 (t80) cc_final: 0.8961 (t80) REVERT: D 717 MET cc_start: 0.7492 (mpp) cc_final: 0.7067 (mtt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.1377 time to fit residues: 113.7993 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 : 0.824 ------------------------------------------------------------------------------- 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: 8.9990 chunk 245 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 220 ASN C 452 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089730 restraints weight = 58925.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092164 restraints weight = 34568.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093825 restraints weight = 23678.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094932 restraints weight = 18034.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095706 restraints weight = 14922.375| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21432 Z= 0.272 Angle : 0.866 9.792 28948 Z= 0.436 Chirality : 0.048 0.224 3292 Planarity : 0.006 0.075 3600 Dihedral : 8.156 59.970 2860 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.41 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -2.26 (0.17), residues: 2556 helix: -0.22 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -3.12 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 714 TYR 0.023 0.003 TYR B 359 PHE 0.029 0.002 PHE C 538 TRP 0.014 0.002 TRP C 692 HIS 0.008 0.002 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00601 (21420) covalent geometry : angle 0.86587 (28948) hydrogen bonds : bond 0.03798 ( 696) hydrogen bonds : angle 4.70638 ( 2028) Misc. bond : bond 0.00116 ( 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 464 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.887 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 321 TYR cc_start: 0.9005 (t80) cc_final: 0.8771 (t80) REVERT: A 440 MET cc_start: 0.8664 (mtt) cc_final: 0.8323 (mmt) REVERT: A 677 MET cc_start: 0.8816 (mmm) cc_final: 0.8507 (mmm) REVERT: B 293 ASP cc_start: 0.8317 (m-30) cc_final: 0.7954 (m-30) REVERT: B 309 ASP cc_start: 0.8231 (m-30) cc_final: 0.8026 (t0) REVERT: B 440 MET cc_start: 0.8694 (mtt) cc_final: 0.8318 (mmt) REVERT: B 555 MET cc_start: 0.8523 (tmm) cc_final: 0.8091 (tmm) REVERT: C 293 ASP cc_start: 0.8285 (m-30) cc_final: 0.7976 (m-30) REVERT: C 304 VAL cc_start: 0.9568 (t) cc_final: 0.9348 (p) REVERT: C 440 MET cc_start: 0.8685 (mtt) cc_final: 0.8324 (mmt) REVERT: C 555 MET cc_start: 0.8507 (tmm) cc_final: 0.8090 (tmm) REVERT: D 293 ASP cc_start: 0.8336 (m-30) cc_final: 0.8002 (m-30) REVERT: D 347 LEU cc_start: 0.9544 (tp) cc_final: 0.9292 (tt) REVERT: D 440 MET cc_start: 0.8668 (mtt) cc_final: 0.8333 (mmt) REVERT: D 555 MET cc_start: 0.8505 (tmm) cc_final: 0.8100 (tmm) REVERT: D 704 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1314 time to fit residues: 100.6657 Evaluate side-chains 355 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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: 8.9990 chunk 166 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 146 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 255 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 346 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 339 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093534 restraints weight = 56688.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096118 restraints weight = 32129.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097819 restraints weight = 21419.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099073 restraints weight = 16079.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099870 restraints weight = 13044.218| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5119 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= 0.148 Angle : 0.779 8.466 28948 Z= 0.385 Chirality : 0.044 0.223 3292 Planarity : 0.005 0.077 3600 Dihedral : 7.872 58.856 2860 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.08 % Favored : 85.76 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -2.11 (0.17), residues: 2556 helix: -0.14 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -3.06 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 TYR 0.017 0.002 TYR A 594 PHE 0.026 0.002 PHE C 538 TRP 0.009 0.001 TRP A 521 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00338 (21420) covalent geometry : angle 0.77883 (28948) hydrogen bonds : bond 0.03284 ( 696) hydrogen bonds : angle 4.32039 ( 2028) Misc. bond : bond 0.00134 ( 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 465 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.878 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: A 293 ASP cc_start: 0.8187 (m-30) cc_final: 0.7825 (m-30) REVERT: A 440 MET cc_start: 0.8571 (mtt) cc_final: 0.8263 (mmp) REVERT: A 555 MET cc_start: 0.8462 (tmm) cc_final: 0.8258 (tmm) REVERT: A 574 MET cc_start: 0.8571 (ppp) cc_final: 0.7814 (ptt) REVERT: A 590 PHE cc_start: 0.8685 (t80) cc_final: 0.8450 (t80) REVERT: A 677 MET cc_start: 0.8854 (mmm) cc_final: 0.8605 (mmm) REVERT: A 706 MET cc_start: 0.8499 (tpp) cc_final: 0.7665 (tpp) REVERT: A 717 MET cc_start: 0.7303 (mpp) cc_final: 0.7091 (mtt) REVERT: B 293 ASP cc_start: 0.8110 (m-30) cc_final: 0.7801 (m-30) REVERT: B 440 MET cc_start: 0.8505 (mtt) cc_final: 0.8296 (mmt) REVERT: B 555 MET cc_start: 0.8513 (tmm) cc_final: 0.8095 (tmm) REVERT: B 672 MET cc_start: 0.8903 (tpp) cc_final: 0.8572 (tpt) REVERT: B 717 MET cc_start: 0.7421 (mpp) cc_final: 0.7060 (mtt) REVERT: C 293 ASP cc_start: 0.8093 (m-30) cc_final: 0.7806 (m-30) REVERT: C 342 LEU cc_start: 0.9027 (mt) cc_final: 0.8607 (mp) REVERT: C 405 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8208 (mp0) REVERT: C 440 MET cc_start: 0.8472 (mtt) cc_final: 0.8270 (mmt) REVERT: C 555 MET cc_start: 0.8486 (tmm) cc_final: 0.8090 (tmm) REVERT: C 717 MET cc_start: 0.7408 (mpp) cc_final: 0.7088 (mtt) REVERT: D 293 ASP cc_start: 0.8090 (m-30) cc_final: 0.7820 (m-30) REVERT: D 321 TYR cc_start: 0.8831 (t80) cc_final: 0.8616 (t80) REVERT: D 440 MET cc_start: 0.8579 (mtt) cc_final: 0.8281 (mmt) REVERT: D 555 MET cc_start: 0.8474 (tmm) cc_final: 0.8068 (tmm) REVERT: D 577 VAL cc_start: 0.9505 (t) cc_final: 0.9300 (p) REVERT: D 590 PHE cc_start: 0.8745 (t80) cc_final: 0.8526 (t80) REVERT: D 704 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8207 (tm-30) REVERT: D 706 MET cc_start: 0.8486 (tpp) cc_final: 0.7625 (tpp) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.1286 time to fit residues: 98.8936 Evaluate side-chains 373 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 163 optimal weight: 30.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN C 580 GLN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094625 restraints weight = 56446.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097170 restraints weight = 32095.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098877 restraints weight = 21513.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100089 restraints weight = 16145.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100907 restraints weight = 13125.888| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5294 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= 0.138 Angle : 0.756 8.955 28948 Z= 0.373 Chirality : 0.043 0.224 3292 Planarity : 0.005 0.078 3600 Dihedral : 7.663 58.936 2860 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.18 % Favored : 84.66 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.69 % 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: -1.96 (0.17), residues: 2556 helix: 0.08 (0.15), residues: 1332 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 363 TYR 0.023 0.002 TYR A 359 PHE 0.027 0.001 PHE C 538 TRP 0.010 0.001 TRP D 521 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00314 (21420) covalent geometry : angle 0.75601 (28948) hydrogen bonds : bond 0.03093 ( 696) hydrogen bonds : angle 4.18885 ( 2028) Misc. bond : bond 0.00128 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.33 seconds wall clock time: 58 minutes 34.23 seconds (3514.23 seconds total)