Starting phenix.real_space_refine on Fri Aug 7 16:44:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lm_77137/08_2026/13lm_77137.map" } resolution = 3.29 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= 0.002 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 S 132 5.16 5 Na 4 4.78 5 C 14748 2.51 5 N 3480 2.21 5 O 3992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22384 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5222 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 18, 'TRANS': 623} Chain breaks: 2 Chain: "B" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5222 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 18, 'TRANS': 623} Chain breaks: 2 Chain: "C" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5222 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 18, 'TRANS': 623} Chain breaks: 2 Chain: "D" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5222 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 18, 'TRANS': 623} Chain breaks: 2 Chain: "A" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 368 Unusual residues: {' NA': 4, 'POV': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.14, per 1000 atoms: 0.18 Number of scatterers: 22384 At special positions: 0 Unit cell: (149.411, 149.411, 125.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 28 15.00 Na 4 11.00 O 3992 8.00 N 3480 7.00 C 14748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 870.6 milliseconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 63.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.738A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.982A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.508A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.605A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.981A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.607A pdb=" N ILE A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.669A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.706A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.652A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.598A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.550A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.573A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.963A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 461 removed outlier: 3.540A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.601A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 507 removed outlier: 4.177A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.718A pdb=" N GLN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.820A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.540A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.935A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.731A pdb=" N GLY A 573 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 574' Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.930A pdb=" N LEU A 584 " --> pdb=" O PRO A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.259A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.917A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.584A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 672 Processing helix chain 'A' and resid 673 through 687 removed outlier: 4.449A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 removed outlier: 3.543A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.617A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.737A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.982A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.508A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.605A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.982A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.607A pdb=" N ILE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.670A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.705A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.652A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.598A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.550A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.573A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.962A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 461 removed outlier: 3.540A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 removed outlier: 3.602A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 507 removed outlier: 4.178A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.719A pdb=" N GLN B 514 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.820A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.541A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 3.934A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.731A pdb=" N GLY B 573 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 578 through 586 removed outlier: 3.931A pdb=" N LEU B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.259A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.917A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.585A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 Processing helix chain 'B' and resid 673 through 687 removed outlier: 4.450A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 706 removed outlier: 3.542A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 738 through 751 removed outlier: 3.617A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.738A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.983A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.508A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.605A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.981A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.607A pdb=" N ILE C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.670A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.706A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.651A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.599A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.550A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.573A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.963A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 461 removed outlier: 3.540A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 494 removed outlier: 3.601A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 507 removed outlier: 4.176A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.718A pdb=" N GLN C 514 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.820A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.541A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 removed outlier: 3.935A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.731A pdb=" N GLY C 573 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET C 574 " --> pdb=" O SER C 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 570 through 574' Processing helix chain 'C' and resid 578 through 586 removed outlier: 3.930A pdb=" N LEU C 584 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.258A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.917A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.584A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 672 Processing helix chain 'C' and resid 673 through 687 removed outlier: 4.450A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 706 removed outlier: 3.543A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 714 through 716 No H-bonds generated for 'chain 'C' and resid 714 through 716' Processing helix chain 'C' and resid 738 through 751 removed outlier: 3.617A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.737A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.983A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.509A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.604A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.981A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 removed outlier: 3.607A pdb=" N ILE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.670A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.706A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.651A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.598A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.551A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.573A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.962A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 461 removed outlier: 3.539A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 494 removed outlier: 3.602A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 507 removed outlier: 4.177A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.719A pdb=" N GLN D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER D 515 " --> pdb=" O ASP D 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 515' Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.820A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.540A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 569 removed outlier: 3.935A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 574 removed outlier: 3.731A pdb=" N GLY D 573 " --> pdb=" O GLN D 570 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET D 574 " --> pdb=" O SER D 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 570 through 574' Processing helix chain 'D' and resid 578 through 586 removed outlier: 3.931A pdb=" N LEU D 584 " --> pdb=" O PRO D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.259A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 605 " --> pdb=" O PHE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.916A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 removed outlier: 3.585A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 Processing helix chain 'D' and resid 673 through 687 removed outlier: 4.450A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 706 removed outlier: 3.543A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 714 through 716 No H-bonds generated for 'chain 'D' and resid 714 through 716' Processing helix chain 'D' and resid 738 through 751 removed outlier: 3.617A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.658A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 723 removed outlier: 3.624A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 380 through 382 removed outlier: 3.658A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 721 through 723 removed outlier: 3.622A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 380 through 382 removed outlier: 3.658A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 721 through 723 removed outlier: 3.623A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 380 through 382 removed outlier: 3.658A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 721 through 723 removed outlier: 3.623A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2388 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: 3.32 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3714 1.32 - 1.45: 5688 1.45 - 1.57: 13098 1.57 - 1.70: 56 1.70 - 1.82: 216 Bond restraints: 22772 Sorted by residual: bond pdb=" O12 POV A1103 " pdb=" P POV A1103 " ideal model delta sigma weight residual 1.657 1.589 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O12 POV B1104 " pdb=" P POV B1104 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O12 POV C1104 " pdb=" P POV C1104 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O12 POV D1106 " pdb=" P POV D1106 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O12 POV B1101 " pdb=" P POV B1101 " ideal model delta sigma weight residual 1.657 1.592 0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 22767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 29445 2.49 - 4.98: 959 4.98 - 7.48: 80 7.48 - 9.97: 32 9.97 - 12.46: 8 Bond angle restraints: 30524 Sorted by residual: angle pdb=" N VAL D 593 " pdb=" CA VAL D 593 " pdb=" C VAL D 593 " ideal model delta sigma weight residual 113.43 107.32 6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N VAL A 593 " pdb=" CA VAL A 593 " pdb=" C VAL A 593 " ideal model delta sigma weight residual 113.43 107.33 6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" N VAL C 593 " pdb=" CA VAL C 593 " pdb=" C VAL C 593 " ideal model delta sigma weight residual 113.43 107.33 6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" N VAL B 593 " pdb=" CA VAL B 593 " pdb=" C VAL B 593 " ideal model delta sigma weight residual 113.43 107.33 6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" C ASN A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.81 -7.35 1.41e+00 5.03e-01 2.72e+01 ... (remaining 30519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 13505 35.33 - 70.66: 371 70.66 - 105.99: 60 105.99 - 141.32: 43 141.32 - 176.65: 13 Dihedral angle restraints: 13992 sinusoidal: 6424 harmonic: 7568 Sorted by residual: dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -158.66 72.66 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS B 721 " pdb=" SG CYS B 721 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -158.63 72.63 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS C 721 " pdb=" SG CYS C 721 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -158.61 72.61 1 1.00e+01 1.00e-02 6.73e+01 ... (remaining 13989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2680 0.065 - 0.129: 530 0.129 - 0.193: 66 0.193 - 0.258: 28 0.258 - 0.322: 8 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CG LEU D 630 " pdb=" CB LEU D 630 " pdb=" CD1 LEU D 630 " pdb=" CD2 LEU D 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU A 630 " pdb=" CB LEU A 630 " pdb=" CD1 LEU A 630 " pdb=" CD2 LEU A 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CG LEU B 630 " pdb=" CB LEU B 630 " pdb=" CD1 LEU B 630 " pdb=" CD2 LEU B 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3309 not shown) Planarity restraints: 3692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 73 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C ARG B 73 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG B 73 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 74 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 73 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C ARG D 73 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG D 73 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 74 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 73 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C ARG A 73 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG A 73 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 74 " -0.014 2.00e-02 2.50e+03 ... (remaining 3689 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 250 2.66 - 3.22: 18788 3.22 - 3.78: 32138 3.78 - 4.34: 46391 4.34 - 4.90: 75588 Nonbonded interactions: 173155 Sorted by model distance: nonbonded pdb="NA NA A1109 " pdb="NA NA A1110 " model vdw 2.097 1.900 nonbonded pdb="NA NA A1109 " pdb="NA NA A1111 " model vdw 2.275 1.900 nonbonded pdb=" OH TYR C 460 " pdb=" O13 POV D1107 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR D 460 " pdb=" O13 POV A1104 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.314 3.040 ... (remaining 173150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 59 through 1107) 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 0.076 22780 Z= 0.341 Angle : 1.027 12.461 30540 Z= 0.506 Chirality : 0.057 0.322 3312 Planarity : 0.006 0.052 3692 Dihedral : 18.642 176.653 9048 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.76 % Favored : 92.77 % Rotamer: Outliers : 0.35 % Allowed : 5.78 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.24 (0.10), residues: 2544 helix: -4.62 (0.05), residues: 1532 sheet: -3.63 (0.68), residues: 40 loop : -2.97 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 226 TYR 0.015 0.003 TYR C 451 PHE 0.023 0.003 PHE B 316 TRP 0.018 0.002 TRP C 742 HIS 0.009 0.002 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.34 (22772) covalent geometry : angle 1.02638 / 0.51 (30524) SS BOND : bond 0.00678 / 0.36 ( 8) SS BOND : angle 1.54992 / 0.90 ( 16) hydrogen bonds : bond 0.35199 / 23.37 ( 824) hydrogen bonds : angle 9.79081 / 6.83 ( 2388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 540 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7960 (mttp) REVERT: A 134 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7809 (tp30) REVERT: A 315 ASP cc_start: 0.6917 (p0) cc_final: 0.6324 (t0) REVERT: A 323 MET cc_start: 0.8061 (ttm) cc_final: 0.7775 (ttm) REVERT: A 327 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7592 (mmm160) REVERT: A 521 TRP cc_start: 0.6921 (t-100) cc_final: 0.6581 (t60) REVERT: A 627 ASP cc_start: 0.7934 (m-30) cc_final: 0.7459 (m-30) REVERT: A 674 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 694 LEU cc_start: 0.8257 (mm) cc_final: 0.7980 (mp) REVERT: A 742 TRP cc_start: 0.7187 (t60) cc_final: 0.6764 (t60) REVERT: B 66 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8141 (mttp) REVERT: B 73 ARG cc_start: 0.5867 (tmt170) cc_final: 0.5491 (ttp80) REVERT: B 134 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8111 (tp30) REVERT: B 255 GLN cc_start: 0.8264 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 273 ASN cc_start: 0.8790 (t0) cc_final: 0.8385 (t0) REVERT: B 293 ASP cc_start: 0.7389 (p0) cc_final: 0.7028 (p0) REVERT: B 315 ASP cc_start: 0.7007 (p0) cc_final: 0.6401 (t0) REVERT: B 386 SER cc_start: 0.8957 (t) cc_final: 0.8741 (p) REVERT: B 501 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 521 TRP cc_start: 0.6751 (t-100) cc_final: 0.6482 (t60) REVERT: B 588 LEU cc_start: 0.8266 (tt) cc_final: 0.7937 (mm) REVERT: B 627 ASP cc_start: 0.7874 (m-30) cc_final: 0.7524 (m-30) REVERT: B 664 LEU cc_start: 0.8530 (tt) cc_final: 0.8281 (tp) REVERT: B 674 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 694 LEU cc_start: 0.8283 (mm) cc_final: 0.7985 (mp) REVERT: B 742 TRP cc_start: 0.7110 (t60) cc_final: 0.6619 (t60) REVERT: C 66 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7946 (mttp) REVERT: C 73 ARG cc_start: 0.5402 (tmt170) cc_final: 0.5155 (ttp80) REVERT: C 134 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7812 (tp30) REVERT: C 315 ASP cc_start: 0.6915 (p0) cc_final: 0.6314 (t0) REVERT: C 327 ARG cc_start: 0.7932 (tpt90) cc_final: 0.7644 (mmm160) REVERT: C 501 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8093 (mm-30) REVERT: C 521 TRP cc_start: 0.6894 (t-100) cc_final: 0.6504 (t60) REVERT: C 588 LEU cc_start: 0.8288 (tt) cc_final: 0.7966 (mm) REVERT: C 627 ASP cc_start: 0.7983 (m-30) cc_final: 0.7548 (m-30) REVERT: C 674 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 694 LEU cc_start: 0.8238 (mm) cc_final: 0.7954 (mp) REVERT: C 722 LYS cc_start: 0.7358 (tmtt) cc_final: 0.7134 (tptt) REVERT: C 742 TRP cc_start: 0.7189 (t60) cc_final: 0.6787 (t60) REVERT: D 66 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7962 (mttp) REVERT: D 73 ARG cc_start: 0.5432 (tmt170) cc_final: 0.5177 (ttp80) REVERT: D 134 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7812 (tp30) REVERT: D 315 ASP cc_start: 0.6921 (p0) cc_final: 0.6324 (t0) REVERT: D 327 ARG cc_start: 0.7918 (tpt90) cc_final: 0.7634 (mmm160) REVERT: D 521 TRP cc_start: 0.6927 (t-100) cc_final: 0.6545 (t60) REVERT: D 627 ASP cc_start: 0.7994 (m-30) cc_final: 0.7523 (m-30) REVERT: D 674 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8144 (mp) REVERT: D 694 LEU cc_start: 0.8258 (mm) cc_final: 0.7979 (mp) REVERT: D 742 TRP cc_start: 0.7225 (t60) cc_final: 0.6822 (t60) outliers start: 8 outliers final: 0 residues processed: 547 average time/residue: 0.1549 time to fit residues: 126.8685 Evaluate side-chains 359 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 355 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 674 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 205 ASN A 297 ASN A 430 HIS A 646 GLN A 647 ASN A 735 ASN B 150 HIS B 205 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 646 GLN B 647 ASN B 735 ASN C 150 HIS C 205 ASN C 256 HIS C 274 GLN C 297 ASN C 430 HIS C 646 GLN C 647 ASN C 735 ASN D 150 HIS D 205 ASN D 256 HIS D 297 ASN D 646 GLN D 647 ASN D 735 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144734 restraints weight = 25046.501| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.92 r_work: 0.3297 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22780 Z= 0.122 Angle : 0.606 6.883 30540 Z= 0.314 Chirality : 0.039 0.165 3312 Planarity : 0.005 0.050 3692 Dihedral : 20.744 178.070 3996 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.50 % Allowed : 10.55 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.14), residues: 2544 helix: -2.75 (0.10), residues: 1564 sheet: -4.17 (0.39), residues: 116 loop : -2.24 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 188 TYR 0.011 0.001 TYR B 451 PHE 0.016 0.001 PHE B 449 TRP 0.016 0.001 TRP B 559 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22772) covalent geometry : angle 0.60592 / 0.31 (30524) SS BOND : bond 0.00031 / 0.02 ( 8) SS BOND : angle 1.02312 / 0.72 ( 16) hydrogen bonds : bond 0.04346 / 2.88 ( 824) hydrogen bonds : angle 4.35327 / 3.07 ( 2388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 380 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8290 (mttp) REVERT: A 315 ASP cc_start: 0.7227 (p0) cc_final: 0.6671 (t0) REVERT: A 327 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7692 (mmm-85) REVERT: A 509 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7404 (ptp90) REVERT: A 627 ASP cc_start: 0.8444 (m-30) cc_final: 0.8162 (m-30) REVERT: A 655 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 694 LEU cc_start: 0.8454 (mm) cc_final: 0.8236 (mp) REVERT: A 737 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8670 (t) REVERT: A 742 TRP cc_start: 0.7224 (t60) cc_final: 0.6984 (t60) REVERT: B 66 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8483 (mttp) REVERT: B 134 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7657 (tp30) REVERT: B 273 ASN cc_start: 0.9077 (t0) cc_final: 0.8856 (t0) REVERT: B 315 ASP cc_start: 0.7223 (p0) cc_final: 0.6655 (t0) REVERT: B 618 ASP cc_start: 0.7589 (t70) cc_final: 0.7233 (m-30) REVERT: B 627 ASP cc_start: 0.8374 (m-30) cc_final: 0.8166 (m-30) REVERT: B 655 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8578 (tp) REVERT: B 694 LEU cc_start: 0.8428 (mm) cc_final: 0.8169 (mp) REVERT: B 742 TRP cc_start: 0.7186 (t60) cc_final: 0.6969 (t60) REVERT: C 66 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8289 (mttp) REVERT: C 73 ARG cc_start: 0.5937 (tmt170) cc_final: 0.5715 (ttp80) REVERT: C 188 ARG cc_start: 0.7459 (mtm110) cc_final: 0.7241 (mtm180) REVERT: C 315 ASP cc_start: 0.7237 (p0) cc_final: 0.6672 (t0) REVERT: C 495 MET cc_start: 0.8399 (mmm) cc_final: 0.8141 (mmm) REVERT: C 509 ARG cc_start: 0.7644 (ptp90) cc_final: 0.7346 (ptp90) REVERT: C 627 ASP cc_start: 0.8468 (m-30) cc_final: 0.8203 (m-30) REVERT: C 655 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8498 (tp) REVERT: C 694 LEU cc_start: 0.8455 (mm) cc_final: 0.8235 (mp) REVERT: C 742 TRP cc_start: 0.7211 (t60) cc_final: 0.6970 (t60) REVERT: D 66 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8313 (mttp) REVERT: D 73 ARG cc_start: 0.5961 (tmt170) cc_final: 0.5719 (ttp80) REVERT: D 188 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7265 (mtm180) REVERT: D 315 ASP cc_start: 0.7256 (p0) cc_final: 0.6664 (t0) REVERT: D 509 ARG cc_start: 0.7677 (ptp90) cc_final: 0.7386 (ptp90) REVERT: D 521 TRP cc_start: 0.7588 (t-100) cc_final: 0.7027 (t60) REVERT: D 627 ASP cc_start: 0.8472 (m-30) cc_final: 0.8193 (m-30) REVERT: D 655 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8552 (tp) REVERT: D 694 LEU cc_start: 0.8453 (mm) cc_final: 0.8233 (mp) REVERT: D 742 TRP cc_start: 0.7237 (t60) cc_final: 0.6965 (t60) outliers start: 57 outliers final: 22 residues processed: 413 average time/residue: 0.1497 time to fit residues: 93.4146 Evaluate side-chains 346 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 319 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 183 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 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 = 0.4067 r_free = 0.4067 target = 0.183327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141190 restraints weight = 25273.787| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.95 r_work: 0.3217 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22780 Z= 0.125 Angle : 0.558 11.032 30540 Z= 0.287 Chirality : 0.039 0.155 3312 Planarity : 0.004 0.043 3692 Dihedral : 19.639 177.280 3988 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.15 % Allowed : 11.60 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.15), residues: 2544 helix: -1.69 (0.12), residues: 1560 sheet: -3.59 (0.43), residues: 96 loop : -2.13 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.014 0.001 TYR B 451 PHE 0.011 0.001 PHE C 449 TRP 0.013 0.001 TRP C 559 HIS 0.002 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22772) covalent geometry : angle 0.55764 / 0.29 (30524) SS BOND : bond 0.00083 / 0.03 ( 8) SS BOND : angle 0.60072 / 0.39 ( 16) hydrogen bonds : bond 0.03793 / 2.51 ( 824) hydrogen bonds : angle 3.91974 / 2.75 ( 2388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 337 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8341 (mttp) REVERT: A 190 LEU cc_start: 0.8776 (mp) cc_final: 0.8556 (mp) REVERT: A 315 ASP cc_start: 0.7241 (p0) cc_final: 0.6640 (t0) REVERT: A 563 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8708 (mp) REVERT: A 627 ASP cc_start: 0.8543 (m-30) cc_final: 0.8295 (m-30) REVERT: A 630 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 655 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 674 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 694 LEU cc_start: 0.8457 (mm) cc_final: 0.8186 (mp) REVERT: A 742 TRP cc_start: 0.7205 (t60) cc_final: 0.6941 (t60) REVERT: B 134 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7570 (tp30) REVERT: B 190 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 315 ASP cc_start: 0.7157 (p0) cc_final: 0.6642 (t0) REVERT: B 618 ASP cc_start: 0.7491 (t70) cc_final: 0.7186 (m-30) REVERT: B 674 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 694 LEU cc_start: 0.8397 (mm) cc_final: 0.8053 (mp) REVERT: C 66 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8297 (mttp) REVERT: C 315 ASP cc_start: 0.7236 (p0) cc_final: 0.6613 (t0) REVERT: C 627 ASP cc_start: 0.8515 (m-30) cc_final: 0.8266 (m-30) REVERT: C 655 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8535 (tp) REVERT: C 674 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8372 (mp) REVERT: C 694 LEU cc_start: 0.8440 (mm) cc_final: 0.8170 (mp) REVERT: C 742 TRP cc_start: 0.7181 (t60) cc_final: 0.6940 (t60) REVERT: D 66 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8326 (mttp) REVERT: D 190 LEU cc_start: 0.8801 (mp) cc_final: 0.8576 (mp) REVERT: D 315 ASP cc_start: 0.7215 (p0) cc_final: 0.6601 (t0) REVERT: D 627 ASP cc_start: 0.8508 (m-30) cc_final: 0.8264 (m-30) REVERT: D 630 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8330 (tp) REVERT: D 655 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (tp) REVERT: D 674 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8400 (mp) REVERT: D 694 LEU cc_start: 0.8445 (mm) cc_final: 0.8184 (mp) REVERT: D 722 LYS cc_start: 0.7292 (tptt) cc_final: 0.6898 (tptt) REVERT: D 742 TRP cc_start: 0.7196 (t60) cc_final: 0.6949 (t60) outliers start: 72 outliers final: 36 residues processed: 385 average time/residue: 0.1526 time to fit residues: 91.2894 Evaluate side-chains 357 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 235 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 164 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.6655 > 50:) chunk 236 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 74 GLN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.184272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142467 restraints weight = 25317.375| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22780 Z= 0.110 Angle : 0.530 11.669 30540 Z= 0.271 Chirality : 0.038 0.164 3312 Planarity : 0.004 0.040 3692 Dihedral : 18.852 172.089 3988 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.06 % Allowed : 13.53 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2544 helix: -1.14 (0.13), residues: 1576 sheet: -3.82 (0.45), residues: 84 loop : -1.83 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.013 0.001 TYR B 451 PHE 0.008 0.001 PHE B 449 TRP 0.011 0.001 TRP D 559 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (22772) covalent geometry : angle 0.53034 / 0.27 (30524) SS BOND : bond 0.00144 / 0.07 ( 8) SS BOND : angle 0.59303 / 0.39 ( 16) hydrogen bonds : bond 0.03154 / 2.09 ( 824) hydrogen bonds : angle 3.81498 / 2.66 ( 2388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 315 ASP cc_start: 0.7306 (p0) cc_final: 0.6680 (t0) REVERT: A 627 ASP cc_start: 0.8524 (m-30) cc_final: 0.8286 (m-30) REVERT: A 630 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 655 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 674 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 694 LEU cc_start: 0.8415 (mm) cc_final: 0.8100 (mp) REVERT: A 742 TRP cc_start: 0.7102 (t60) cc_final: 0.6901 (t60) REVERT: B 134 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7512 (tp30) REVERT: B 190 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 315 ASP cc_start: 0.7222 (p0) cc_final: 0.6675 (t0) REVERT: B 618 ASP cc_start: 0.7551 (t70) cc_final: 0.7180 (m-30) REVERT: B 674 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 694 LEU cc_start: 0.8436 (mm) cc_final: 0.8115 (mp) REVERT: B 722 LYS cc_start: 0.7377 (tptt) cc_final: 0.6978 (tptt) REVERT: C 315 ASP cc_start: 0.7252 (p0) cc_final: 0.6640 (t0) REVERT: C 618 ASP cc_start: 0.7265 (t70) cc_final: 0.7005 (m-30) REVERT: C 627 ASP cc_start: 0.8540 (m-30) cc_final: 0.8293 (m-30) REVERT: C 674 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 694 LEU cc_start: 0.8404 (mm) cc_final: 0.8091 (mp) REVERT: D 315 ASP cc_start: 0.7254 (p0) cc_final: 0.6644 (t0) REVERT: D 430 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7393 (t-90) REVERT: D 627 ASP cc_start: 0.8531 (m-30) cc_final: 0.8297 (m-30) REVERT: D 655 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8577 (tp) REVERT: D 674 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8399 (mp) REVERT: D 694 LEU cc_start: 0.8397 (mm) cc_final: 0.8091 (mp) REVERT: D 722 LYS cc_start: 0.7474 (tptt) cc_final: 0.7254 (tptp) REVERT: D 723 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.5243 (t) outliers start: 70 outliers final: 38 residues processed: 360 average time/residue: 0.1441 time to fit residues: 80.9797 Evaluate side-chains 323 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 225 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139806 restraints weight = 25039.697| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.88 r_work: 0.3190 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22780 Z= 0.148 Angle : 0.556 7.737 30540 Z= 0.283 Chirality : 0.040 0.157 3312 Planarity : 0.004 0.040 3692 Dihedral : 18.434 172.431 3988 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.58 % Allowed : 14.67 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2544 helix: -0.83 (0.13), residues: 1576 sheet: -3.53 (0.44), residues: 92 loop : -1.75 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 696 TYR 0.017 0.002 TYR B 451 PHE 0.010 0.001 PHE C 590 TRP 0.011 0.001 TRP B 559 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (22772) covalent geometry : angle 0.55580 / 0.28 (30524) SS BOND : bond 0.00084 / 0.03 ( 8) SS BOND : angle 0.56600 / 0.35 ( 16) hydrogen bonds : bond 0.03396 / 2.24 ( 824) hydrogen bonds : angle 3.79940 / 2.66 ( 2388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 315 ASP cc_start: 0.7301 (p0) cc_final: 0.6645 (t0) REVERT: A 512 ASP cc_start: 0.7801 (m-30) cc_final: 0.7526 (m-30) REVERT: A 627 ASP cc_start: 0.8533 (m-30) cc_final: 0.8293 (m-30) REVERT: A 655 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 674 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 694 LEU cc_start: 0.8405 (mm) cc_final: 0.8073 (mp) REVERT: A 742 TRP cc_start: 0.7160 (t60) cc_final: 0.6921 (t60) REVERT: B 134 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7515 (tp30) REVERT: B 190 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 288 ASP cc_start: 0.8261 (m-30) cc_final: 0.8029 (t0) REVERT: B 355 GLU cc_start: 0.8693 (tp30) cc_final: 0.8390 (mm-30) REVERT: B 674 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 694 LEU cc_start: 0.8430 (mm) cc_final: 0.8071 (mp) REVERT: C 315 ASP cc_start: 0.7306 (p0) cc_final: 0.6644 (t0) REVERT: C 512 ASP cc_start: 0.7828 (m-30) cc_final: 0.7564 (m-30) REVERT: C 618 ASP cc_start: 0.7406 (t70) cc_final: 0.7009 (m-30) REVERT: C 627 ASP cc_start: 0.8547 (m-30) cc_final: 0.8314 (m-30) REVERT: C 674 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8392 (mp) REVERT: C 694 LEU cc_start: 0.8422 (mm) cc_final: 0.8087 (mp) REVERT: D 190 LEU cc_start: 0.8799 (mp) cc_final: 0.8579 (mp) REVERT: D 315 ASP cc_start: 0.7308 (p0) cc_final: 0.6627 (t0) REVERT: D 512 ASP cc_start: 0.7788 (m-30) cc_final: 0.7519 (m-30) REVERT: D 627 ASP cc_start: 0.8556 (m-30) cc_final: 0.8328 (m-30) REVERT: D 655 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 674 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 694 LEU cc_start: 0.8423 (mm) cc_final: 0.8083 (mp) REVERT: D 722 LYS cc_start: 0.7547 (tptt) cc_final: 0.7303 (tptp) REVERT: D 723 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5258 (t) outliers start: 59 outliers final: 34 residues processed: 338 average time/residue: 0.1420 time to fit residues: 74.9291 Evaluate side-chains 327 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 94 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 159 optimal weight: 0.0020 chunk 57 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138747 restraints weight = 25254.525| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.04 r_work: 0.3189 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22780 Z= 0.141 Angle : 0.541 6.407 30540 Z= 0.277 Chirality : 0.039 0.149 3312 Planarity : 0.004 0.040 3692 Dihedral : 17.757 175.250 3988 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.76 % Allowed : 14.67 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.17), residues: 2544 helix: -0.59 (0.13), residues: 1576 sheet: -4.03 (0.37), residues: 116 loop : -1.65 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.016 0.001 TYR A 451 PHE 0.013 0.001 PHE B 506 TRP 0.010 0.001 TRP A 559 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (22772) covalent geometry : angle 0.54106 / 0.28 (30524) SS BOND : bond 0.00103 / 0.04 ( 8) SS BOND : angle 0.90489 / 0.52 ( 16) hydrogen bonds : bond 0.03210 / 2.12 ( 824) hydrogen bonds : angle 3.70755 / 2.59 ( 2388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 315 ASP cc_start: 0.7354 (p0) cc_final: 0.6680 (t0) REVERT: A 512 ASP cc_start: 0.7880 (m-30) cc_final: 0.7576 (m-30) REVERT: A 627 ASP cc_start: 0.8523 (m-30) cc_final: 0.8304 (m-30) REVERT: A 655 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 674 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 694 LEU cc_start: 0.8425 (mm) cc_final: 0.8092 (mp) REVERT: A 742 TRP cc_start: 0.7164 (t60) cc_final: 0.6961 (t60) REVERT: B 134 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7554 (tp30) REVERT: B 190 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 234 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 288 ASP cc_start: 0.8267 (m-30) cc_final: 0.8021 (t0) REVERT: B 674 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 694 LEU cc_start: 0.8409 (mm) cc_final: 0.8062 (mp) REVERT: C 315 ASP cc_start: 0.7369 (p0) cc_final: 0.6671 (t0) REVERT: C 627 ASP cc_start: 0.8550 (m-30) cc_final: 0.8328 (m-30) REVERT: C 674 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 694 LEU cc_start: 0.8430 (mm) cc_final: 0.8098 (mp) REVERT: D 190 LEU cc_start: 0.8788 (mp) cc_final: 0.8559 (mp) REVERT: D 315 ASP cc_start: 0.7353 (p0) cc_final: 0.6672 (t0) REVERT: D 512 ASP cc_start: 0.7884 (m-30) cc_final: 0.7580 (m-30) REVERT: D 627 ASP cc_start: 0.8535 (m-30) cc_final: 0.8319 (m-30) REVERT: D 655 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 674 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8409 (mp) REVERT: D 694 LEU cc_start: 0.8427 (mm) cc_final: 0.8098 (mp) REVERT: D 722 LYS cc_start: 0.7478 (tptt) cc_final: 0.7262 (tptp) REVERT: D 723 VAL cc_start: 0.5465 (OUTLIER) cc_final: 0.5104 (t) outliers start: 63 outliers final: 40 residues processed: 347 average time/residue: 0.1446 time to fit residues: 78.7539 Evaluate side-chains 326 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 232 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 220 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135363 restraints weight = 25328.590| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.91 r_work: 0.3141 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22780 Z= 0.198 Angle : 0.602 7.046 30540 Z= 0.306 Chirality : 0.042 0.160 3312 Planarity : 0.004 0.041 3692 Dihedral : 17.655 161.235 3988 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.02 % Allowed : 14.40 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2544 helix: -0.59 (0.13), residues: 1572 sheet: -4.07 (0.36), residues: 116 loop : -1.67 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.020 0.002 TYR C 451 PHE 0.013 0.001 PHE B 590 TRP 0.012 0.001 TRP B 559 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (22772) covalent geometry : angle 0.60222 / 0.31 (30524) SS BOND : bond 0.00252 / 0.10 ( 8) SS BOND : angle 0.87784 / 0.44 ( 16) hydrogen bonds : bond 0.03679 / 2.43 ( 824) hydrogen bonds : angle 3.86440 / 2.70 ( 2388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 315 ASP cc_start: 0.7374 (p0) cc_final: 0.6647 (t0) REVERT: A 627 ASP cc_start: 0.8566 (m-30) cc_final: 0.8329 (m-30) REVERT: A 655 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 674 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 694 LEU cc_start: 0.8471 (mm) cc_final: 0.8121 (mp) REVERT: A 722 LYS cc_start: 0.7447 (tptt) cc_final: 0.7159 (tptp) REVERT: A 742 TRP cc_start: 0.7083 (t60) cc_final: 0.6871 (t60) REVERT: B 134 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7626 (tp30) REVERT: B 190 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 288 ASP cc_start: 0.8311 (m-30) cc_final: 0.7957 (t0) REVERT: B 355 GLU cc_start: 0.8747 (tp30) cc_final: 0.8546 (mm-30) REVERT: B 674 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 694 LEU cc_start: 0.8478 (mm) cc_final: 0.8121 (mp) REVERT: B 722 LYS cc_start: 0.7356 (tptp) cc_final: 0.6864 (tptt) REVERT: C 315 ASP cc_start: 0.7351 (p0) cc_final: 0.6645 (t0) REVERT: C 563 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8873 (mp) REVERT: C 627 ASP cc_start: 0.8573 (m-30) cc_final: 0.8352 (m-30) REVERT: C 649 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8440 (tppp) REVERT: C 674 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 694 LEU cc_start: 0.8488 (mm) cc_final: 0.8142 (mp) REVERT: C 722 LYS cc_start: 0.7453 (tptt) cc_final: 0.6916 (tptt) REVERT: D 190 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 315 ASP cc_start: 0.7334 (p0) cc_final: 0.6633 (t0) REVERT: D 627 ASP cc_start: 0.8561 (m-30) cc_final: 0.8323 (m-30) REVERT: D 655 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8616 (tp) REVERT: D 674 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8408 (mp) REVERT: D 694 LEU cc_start: 0.8484 (mm) cc_final: 0.8141 (mp) REVERT: D 722 LYS cc_start: 0.7512 (tptt) cc_final: 0.7000 (tptt) REVERT: D 723 VAL cc_start: 0.5389 (OUTLIER) cc_final: 0.4950 (t) outliers start: 69 outliers final: 42 residues processed: 344 average time/residue: 0.1595 time to fit residues: 85.2953 Evaluate side-chains 337 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 161 optimal weight: 3.9990 chunk 251 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 182 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 182 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 410 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.184274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144369 restraints weight = 25016.402| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.79 r_work: 0.3223 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22780 Z= 0.091 Angle : 0.516 11.427 30540 Z= 0.263 Chirality : 0.038 0.148 3312 Planarity : 0.003 0.040 3692 Dihedral : 16.471 119.947 3988 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.23 % Allowed : 15.15 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2544 helix: -0.12 (0.13), residues: 1552 sheet: -3.68 (0.46), residues: 84 loop : -1.59 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.011 0.001 TYR D 564 PHE 0.011 0.001 PHE B 506 TRP 0.008 0.001 TRP A 380 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (22772) covalent geometry : angle 0.51522 / 0.26 (30524) SS BOND : bond 0.00161 / 0.09 ( 8) SS BOND : angle 0.91145 / 0.51 ( 16) hydrogen bonds : bond 0.02709 / 1.78 ( 824) hydrogen bonds : angle 3.60517 / 2.52 ( 2388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 0.735 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: A 190 LEU cc_start: 0.8781 (mp) cc_final: 0.8477 (mp) REVERT: A 255 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 315 ASP cc_start: 0.7278 (p0) cc_final: 0.6721 (t0) REVERT: A 512 ASP cc_start: 0.7863 (m-30) cc_final: 0.7618 (m-30) REVERT: A 674 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 694 LEU cc_start: 0.8352 (mm) cc_final: 0.8028 (mp) REVERT: B 134 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7603 (tp30) REVERT: B 190 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8642 (mp) REVERT: B 315 ASP cc_start: 0.7215 (p0) cc_final: 0.6742 (t0) REVERT: B 320 MET cc_start: 0.8444 (mmm) cc_final: 0.8159 (mmm) REVERT: B 674 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 694 LEU cc_start: 0.8355 (mm) cc_final: 0.8018 (mp) REVERT: B 723 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5248 (t) REVERT: C 255 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 315 ASP cc_start: 0.7247 (p0) cc_final: 0.6701 (t0) REVERT: C 627 ASP cc_start: 0.8493 (m-30) cc_final: 0.8293 (m-30) REVERT: C 674 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 694 LEU cc_start: 0.8373 (mm) cc_final: 0.8057 (mp) REVERT: C 722 LYS cc_start: 0.7460 (tptt) cc_final: 0.7253 (tptp) REVERT: D 190 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 255 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8264 (tm-30) REVERT: D 315 ASP cc_start: 0.7217 (p0) cc_final: 0.6702 (t0) REVERT: D 512 ASP cc_start: 0.7840 (m-30) cc_final: 0.7598 (m-30) REVERT: D 610 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7688 (mt-10) REVERT: D 649 LYS cc_start: 0.8662 (tppp) cc_final: 0.7723 (ptpp) REVERT: D 655 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8538 (tp) REVERT: D 674 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 694 LEU cc_start: 0.8355 (mm) cc_final: 0.8041 (mp) REVERT: D 722 LYS cc_start: 0.7517 (tptt) cc_final: 0.6980 (tptt) REVERT: D 723 VAL cc_start: 0.5094 (OUTLIER) cc_final: 0.4673 (t) outliers start: 51 outliers final: 39 residues processed: 360 average time/residue: 0.1571 time to fit residues: 87.2947 Evaluate side-chains 340 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 19 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138872 restraints weight = 25262.893| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.94 r_work: 0.3172 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22780 Z= 0.137 Angle : 0.560 10.760 30540 Z= 0.285 Chirality : 0.040 0.145 3312 Planarity : 0.003 0.041 3692 Dihedral : 16.291 107.286 3988 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.41 % Allowed : 15.98 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2544 helix: -0.04 (0.13), residues: 1552 sheet: -3.42 (0.43), residues: 96 loop : -1.64 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.016 0.001 TYR C 451 PHE 0.010 0.001 PHE C 526 TRP 0.014 0.001 TRP B 559 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (22772) covalent geometry : angle 0.55972 / 0.28 (30524) SS BOND : bond 0.00478 / 0.13 ( 8) SS BOND : angle 1.18095 / 0.62 ( 16) hydrogen bonds : bond 0.03073 / 2.03 ( 824) hydrogen bonds : angle 3.71527 / 2.59 ( 2388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8809 (mp) cc_final: 0.8495 (mp) REVERT: A 255 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 512 ASP cc_start: 0.7894 (m-30) cc_final: 0.7603 (m-30) REVERT: A 674 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 694 LEU cc_start: 0.8414 (mm) cc_final: 0.8066 (mp) REVERT: A 722 LYS cc_start: 0.7431 (tptp) cc_final: 0.6971 (tptt) REVERT: B 134 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7674 (tp30) REVERT: B 355 GLU cc_start: 0.8695 (tp30) cc_final: 0.8419 (mm-30) REVERT: B 512 ASP cc_start: 0.7744 (m-30) cc_final: 0.7397 (m-30) REVERT: B 674 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8382 (mp) REVERT: B 694 LEU cc_start: 0.8411 (mm) cc_final: 0.8041 (mp) REVERT: B 722 LYS cc_start: 0.7373 (tptp) cc_final: 0.6961 (tptt) REVERT: B 723 VAL cc_start: 0.5493 (OUTLIER) cc_final: 0.5236 (t) REVERT: C 255 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 627 ASP cc_start: 0.8497 (m-30) cc_final: 0.8288 (m-30) REVERT: C 674 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8436 (mp) REVERT: C 694 LEU cc_start: 0.8425 (mm) cc_final: 0.8076 (mp) REVERT: C 722 LYS cc_start: 0.7534 (tptt) cc_final: 0.7313 (tptp) REVERT: D 190 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8507 (mp) REVERT: D 255 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 512 ASP cc_start: 0.7870 (m-30) cc_final: 0.7581 (m-30) REVERT: D 655 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 674 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8392 (mp) REVERT: D 694 LEU cc_start: 0.8420 (mm) cc_final: 0.8077 (mp) REVERT: D 722 LYS cc_start: 0.7544 (tptt) cc_final: 0.7022 (tptt) REVERT: D 723 VAL cc_start: 0.5049 (OUTLIER) cc_final: 0.4581 (t) outliers start: 55 outliers final: 40 residues processed: 325 average time/residue: 0.1625 time to fit residues: 81.2063 Evaluate side-chains 320 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 219 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138586 restraints weight = 25352.612| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.00 r_work: 0.3178 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22780 Z= 0.142 Angle : 0.568 10.256 30540 Z= 0.289 Chirality : 0.040 0.158 3312 Planarity : 0.003 0.041 3692 Dihedral : 16.119 106.069 3988 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.45 % Allowed : 16.02 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2544 helix: 0.00 (0.13), residues: 1552 sheet: -3.37 (0.43), residues: 96 loop : -1.71 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.016 0.001 TYR C 451 PHE 0.011 0.001 PHE B 506 TRP 0.012 0.001 TRP B 559 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (22772) covalent geometry : angle 0.56754 / 0.29 (30524) SS BOND : bond 0.00225 / 0.07 ( 8) SS BOND : angle 1.40231 / 0.61 ( 16) hydrogen bonds : bond 0.03084 / 2.04 ( 824) hydrogen bonds : angle 3.74177 / 2.61 ( 2388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8788 (mp) cc_final: 0.8450 (mp) REVERT: A 255 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 315 ASP cc_start: 0.7376 (p0) cc_final: 0.6756 (t0) REVERT: A 320 MET cc_start: 0.8599 (mmm) cc_final: 0.8185 (mmm) REVERT: A 674 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 694 LEU cc_start: 0.8403 (mm) cc_final: 0.8051 (mp) REVERT: A 722 LYS cc_start: 0.7457 (tptp) cc_final: 0.6952 (tptt) REVERT: B 134 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7686 (tp30) REVERT: B 674 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 694 LEU cc_start: 0.8400 (mm) cc_final: 0.8042 (mp) REVERT: B 722 LYS cc_start: 0.7427 (tptp) cc_final: 0.6956 (tptt) REVERT: B 723 VAL cc_start: 0.5556 (OUTLIER) cc_final: 0.5292 (t) REVERT: C 255 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 315 ASP cc_start: 0.7387 (p0) cc_final: 0.6751 (t0) REVERT: C 674 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 694 LEU cc_start: 0.8436 (mm) cc_final: 0.8101 (mp) REVERT: C 722 LYS cc_start: 0.7586 (tptt) cc_final: 0.7364 (tptp) REVERT: D 190 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8490 (mp) REVERT: D 255 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 315 ASP cc_start: 0.7386 (p0) cc_final: 0.6730 (t0) REVERT: D 655 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8571 (tp) REVERT: D 674 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 694 LEU cc_start: 0.8407 (mm) cc_final: 0.8068 (mp) REVERT: D 722 LYS cc_start: 0.7558 (tptt) cc_final: 0.7018 (tptt) REVERT: D 723 VAL cc_start: 0.5147 (OUTLIER) cc_final: 0.4734 (t) outliers start: 56 outliers final: 42 residues processed: 318 average time/residue: 0.1627 time to fit residues: 79.5485 Evaluate side-chains 321 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 229 optimal weight: 0.0060 chunk 78 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 188 optimal weight: 0.0570 chunk 94 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.185885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145438 restraints weight = 25237.254| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.86 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22780 Z= 0.092 Angle : 0.524 10.645 30540 Z= 0.267 Chirality : 0.038 0.261 3312 Planarity : 0.003 0.040 3692 Dihedral : 15.389 103.325 3988 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.15 % Allowed : 16.42 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2544 helix: 0.33 (0.13), residues: 1544 sheet: -3.45 (0.49), residues: 84 loop : -1.68 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.011 0.001 TYR D 564 PHE 0.014 0.001 PHE B 506 TRP 0.008 0.001 TRP A 380 HIS 0.003 0.000 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (22772) covalent geometry : angle 0.52379 / 0.27 (30524) SS BOND : bond 0.00183 / 0.10 ( 8) SS BOND : angle 1.15243 / 0.63 ( 16) hydrogen bonds : bond 0.02501 / 1.65 ( 824) hydrogen bonds : angle 3.51996 / 2.44 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6323.70 seconds wall clock time: 108 minutes 39.79 seconds (6519.79 seconds total)