Starting phenix.real_space_refine on Thu Mar 5 10:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugg_26488/03_2026/7ugg_26488.cif" } resolution = 3.16 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= 0.023 sd= 0.102 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 24 5.49 5 S 116 5.16 5 Na 2 4.78 5 C 14260 2.51 5 N 3348 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21670 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 355 Unusual residues: {' NA': 1, 'N8R': 2, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 333 Unusual residues: {'N8R': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 334 Unusual residues: {' NA': 1, 'N8R': 1, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 4.72, per 1000 atoms: 0.22 Number of scatterers: 21670 At special positions: 0 Unit cell: (147.06, 147.06, 122.98, 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 116 16.00 P 24 15.00 Na 2 11.00 O 3920 8.00 N 3348 7.00 C 14260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 960.5 milliseconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4744 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 63.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.626A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.583A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.507A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.644A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.643A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.672A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.977A pdb=" N GLY A 258 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.748A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.741A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.626A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.944A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.705A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.153A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 461 removed outlier: 3.551A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 3.621A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 4.235A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 517' Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.945A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.764A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.743A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.723A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.757A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.661A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.830A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.655A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.889A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.927A pdb=" N GLN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.731A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.625A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.583A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.506A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.645A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.642A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.672A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.977A pdb=" N GLY B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.747A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.741A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.627A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.944A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.705A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.154A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.550A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.621A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 4.235A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 517' Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.946A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 541 removed outlier: 3.764A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.743A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.723A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.757A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.660A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.830A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 655 through 667 removed outlier: 3.655A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.888A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.927A pdb=" N GLN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.731A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.624A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.583A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.506A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.645A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.642A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.672A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.977A pdb=" N GLY C 258 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.748A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.741A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.627A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.943A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.705A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.153A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 461 removed outlier: 3.550A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.620A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 4.235A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 517' Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.946A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 541 removed outlier: 3.764A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.743A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.722A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.756A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.660A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.830A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.655A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.889A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.926A pdb=" N GLN C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.732A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.625A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.582A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.506A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.645A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.642A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.672A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.977A pdb=" N GLY D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.748A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.741A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.626A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.944A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.704A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.153A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 461 removed outlier: 3.550A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 3.620A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 517 removed outlier: 4.236A pdb=" N ILE D 516 " --> pdb=" O ASP D 512 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 517' Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.945A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 541 removed outlier: 3.763A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.743A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.723A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.756A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 604 removed outlier: 3.661A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.830A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 655 through 667 removed outlier: 3.655A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.889A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 704 removed outlier: 3.926A pdb=" N GLN D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.732A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.932A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.932A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.933A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.931A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2322 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: 3.15 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3284 1.30 - 1.43: 5668 1.43 - 1.55: 12639 1.55 - 1.68: 177 1.68 - 1.81: 196 Bond restraints: 21964 Sorted by residual: bond pdb=" C09 N8R B 907 " pdb=" C10 N8R B 907 " ideal model delta sigma weight residual 1.377 1.539 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C09 N8R A 905 " pdb=" C10 N8R A 905 " ideal model delta sigma weight residual 1.377 1.539 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C09 N8R A 907 " pdb=" C10 N8R A 907 " ideal model delta sigma weight residual 1.377 1.538 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" C09 N8R D 907 " pdb=" C10 N8R D 907 " ideal model delta sigma weight residual 1.377 1.537 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C18 N8R A 907 " pdb=" N01 N8R A 907 " ideal model delta sigma weight residual 1.463 1.309 0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 21959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 28217 2.80 - 5.61: 906 5.61 - 8.41: 226 8.41 - 11.21: 89 11.21 - 14.02: 46 Bond angle restraints: 29484 Sorted by residual: angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" C VAL B 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL D 248 " pdb=" CA VAL D 248 " pdb=" C VAL D 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL C 248 " pdb=" CA VAL C 248 " pdb=" C VAL C 248 " ideal model delta sigma weight residual 112.96 106.37 6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 112.96 106.40 6.56 1.00e+00 1.00e+00 4.30e+01 angle pdb=" N GLY A 602 " pdb=" CA GLY A 602 " pdb=" C GLY A 602 " ideal model delta sigma weight residual 112.50 118.44 -5.94 1.16e+00 7.43e-01 2.62e+01 ... (remaining 29479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 12845 35.74 - 71.47: 457 71.47 - 107.21: 62 107.21 - 142.94: 28 142.94 - 178.68: 8 Dihedral angle restraints: 13400 sinusoidal: 6092 harmonic: 7308 Sorted by residual: dihedral pdb=" CA ASP B 315 " pdb=" C ASP B 315 " pdb=" N PHE B 316 " pdb=" CA PHE B 316 " ideal model delta harmonic sigma weight residual 180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP A 315 " pdb=" C ASP A 315 " pdb=" N PHE A 316 " pdb=" CA PHE A 316 " ideal model delta harmonic sigma weight residual -180.00 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP D 315 " pdb=" C ASP D 315 " pdb=" N PHE D 316 " pdb=" CA PHE D 316 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 13397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2769 0.073 - 0.146: 442 0.146 - 0.218: 17 0.218 - 0.291: 0 0.291 - 0.364: 4 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 475 " pdb=" CB LEU D 475 " pdb=" CD1 LEU D 475 " pdb=" CD2 LEU D 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU C 475 " pdb=" CB LEU C 475 " pdb=" CD1 LEU C 475 " pdb=" CD2 LEU C 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3229 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.11e+00 pdb=" CG PHE A 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE C 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 526 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 526 " -0.012 2.00e-02 2.50e+03 2.14e-02 7.98e+00 pdb=" CG PHE D 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 526 " -0.006 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2022 2.73 - 3.27: 19061 3.27 - 3.82: 31567 3.82 - 4.36: 40083 4.36 - 4.90: 69755 Nonbonded interactions: 162488 Sorted by model distance: nonbonded pdb=" OH TYR C 213 " pdb=" O PRO D 753 " model vdw 2.192 3.040 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR D 213 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO B 753 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 213 " pdb=" O PRO C 753 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 321 " pdb=" OE2 GLU A 334 " model vdw 2.304 3.040 ... (remaining 162483 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 118 through 904 or resid 906)) selection = (chain 'B' and (resid 118 through 904 or resid 906)) selection = (chain 'C' and (resid 118 through 904 or resid 906)) selection = (chain 'D' and (resid 118 through 904 or resid 906)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.162 21964 Z= 0.563 Angle : 1.445 14.018 29484 Z= 0.704 Chirality : 0.052 0.364 3232 Planarity : 0.007 0.064 3556 Dihedral : 18.879 178.679 8656 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.17 % Favored : 92.51 % Rotamer: Outliers : 0.54 % Allowed : 2.72 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -6.21 (0.11), residues: 2456 helix: -4.58 (0.06), residues: 1448 sheet: -4.46 (0.35), residues: 96 loop : -2.86 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 363 TYR 0.024 0.004 TYR D 390 PHE 0.044 0.003 PHE A 526 TRP 0.021 0.003 TRP C 493 HIS 0.008 0.002 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.01202 (21964) covalent geometry : angle 1.44510 (29484) hydrogen bonds : bond 0.37209 ( 798) hydrogen bonds : angle 10.49589 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 411 time to evaluate : 0.578 Fit side-chains REVERT: A 581 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7426 (mptt) REVERT: B 581 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7400 (mptt) REVERT: B 653 LEU cc_start: 0.5802 (tp) cc_final: 0.4930 (mp) REVERT: C 143 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8279 (tp-100) REVERT: C 581 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7327 (mptt) REVERT: C 653 LEU cc_start: 0.5789 (tp) cc_final: 0.5008 (mp) outliers start: 12 outliers final: 0 residues processed: 419 average time/residue: 0.1425 time to fit residues: 94.5772 Evaluate side-chains 257 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 255 GLN A 471 HIS A 477 HIS A 643 ASN A 671 ASN A 745 HIS B 140 GLN B 178 ASN B 255 GLN B 477 HIS B 647 ASN B 671 ASN B 745 HIS C 178 ASN C 255 GLN C 477 HIS C 647 ASN C 671 ASN C 745 HIS D 143 GLN D 178 ASN D 255 GLN D 477 HIS D 745 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111890 restraints weight = 32997.336| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.32 r_work: 0.3180 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21964 Z= 0.144 Angle : 0.649 8.695 29484 Z= 0.333 Chirality : 0.040 0.170 3232 Planarity : 0.005 0.047 3556 Dihedral : 22.045 159.719 3812 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.58 % Favored : 94.10 % Rotamer: Outliers : 1.95 % Allowed : 7.67 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.33 (0.13), residues: 2456 helix: -2.70 (0.10), residues: 1488 sheet: -3.69 (0.32), residues: 112 loop : -2.71 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.017 0.002 TYR D 390 PHE 0.013 0.001 PHE C 316 TRP 0.012 0.002 TRP A 559 HIS 0.009 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00323 (21964) covalent geometry : angle 0.64906 (29484) hydrogen bonds : bond 0.05168 ( 798) hydrogen bonds : angle 4.53081 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.780 Fit side-chains REVERT: A 544 TYR cc_start: 0.6470 (m-80) cc_final: 0.6189 (m-80) REVERT: A 570 GLN cc_start: 0.7982 (tt0) cc_final: 0.7709 (tt0) REVERT: A 650 TYR cc_start: 0.5839 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: B 159 MET cc_start: 0.7851 (mmp) cc_final: 0.7623 (mmm) REVERT: B 211 GLU cc_start: 0.7868 (pm20) cc_final: 0.7562 (pm20) REVERT: B 544 TYR cc_start: 0.6549 (m-80) cc_final: 0.6234 (m-80) REVERT: B 570 GLN cc_start: 0.7910 (tt0) cc_final: 0.7657 (tt0) REVERT: B 581 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6850 (mptt) REVERT: B 726 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 531 VAL cc_start: 0.8603 (t) cc_final: 0.8288 (m) REVERT: C 544 TYR cc_start: 0.6516 (m-80) cc_final: 0.6205 (m-80) REVERT: C 570 GLN cc_start: 0.7874 (tt0) cc_final: 0.7602 (tt0) REVERT: C 581 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6909 (mptt) REVERT: D 544 TYR cc_start: 0.6276 (m-80) cc_final: 0.5908 (m-80) REVERT: D 570 GLN cc_start: 0.8199 (tt0) cc_final: 0.7896 (tt0) REVERT: D 650 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5076 (m-10) outliers start: 43 outliers final: 12 residues processed: 324 average time/residue: 0.1382 time to fit residues: 70.8572 Evaluate side-chains 260 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 246 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109797 restraints weight = 32783.525| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.43 r_work: 0.3129 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21964 Z= 0.164 Angle : 0.635 8.197 29484 Z= 0.321 Chirality : 0.041 0.175 3232 Planarity : 0.004 0.048 3556 Dihedral : 20.290 123.508 3812 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.47 % Favored : 93.20 % Rotamer: Outliers : 1.95 % Allowed : 8.58 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.19 (0.15), residues: 2456 helix: -1.62 (0.12), residues: 1512 sheet: -3.32 (0.34), residues: 108 loop : -2.61 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 319 TYR 0.022 0.002 TYR B 390 PHE 0.015 0.001 PHE A 316 TRP 0.008 0.001 TRP C 692 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00389 (21964) covalent geometry : angle 0.63514 (29484) hydrogen bonds : bond 0.05015 ( 798) hydrogen bonds : angle 4.18084 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.805 Fit side-chains REVERT: A 544 TYR cc_start: 0.6450 (m-80) cc_final: 0.6195 (m-80) REVERT: A 650 TYR cc_start: 0.5784 (OUTLIER) cc_final: 0.5298 (m-80) REVERT: B 211 GLU cc_start: 0.7894 (pm20) cc_final: 0.7488 (pm20) REVERT: B 544 TYR cc_start: 0.6411 (m-80) cc_final: 0.6173 (m-80) REVERT: B 581 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6860 (mptt) REVERT: B 650 TYR cc_start: 0.5983 (OUTLIER) cc_final: 0.5306 (m-80) REVERT: B 726 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 211 GLU cc_start: 0.7823 (pm20) cc_final: 0.7548 (pm20) REVERT: C 540 TYR cc_start: 0.8400 (t80) cc_final: 0.7853 (t80) REVERT: C 544 TYR cc_start: 0.6416 (m-80) cc_final: 0.6193 (m-80) REVERT: C 581 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6820 (mptt) REVERT: C 650 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: C 653 LEU cc_start: 0.5366 (tt) cc_final: 0.5091 (mm) REVERT: D 544 TYR cc_start: 0.6335 (m-80) cc_final: 0.6029 (m-80) REVERT: D 581 LYS cc_start: 0.7082 (mmtt) cc_final: 0.6723 (mptt) REVERT: D 650 TYR cc_start: 0.5581 (OUTLIER) cc_final: 0.4948 (m-80) outliers start: 43 outliers final: 28 residues processed: 298 average time/residue: 0.1416 time to fit residues: 67.1876 Evaluate side-chains 265 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 99 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 23 optimal weight: 0.0570 chunk 177 optimal weight: 0.7980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 695 GLN B 227 GLN B 695 GLN C 227 GLN D 227 GLN D 255 GLN D 695 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114024 restraints weight = 32946.481| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.33 r_work: 0.3208 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21964 Z= 0.098 Angle : 0.548 8.390 29484 Z= 0.279 Chirality : 0.038 0.163 3232 Planarity : 0.003 0.041 3556 Dihedral : 18.845 103.668 3812 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.37 % Favored : 94.34 % Rotamer: Outliers : 2.13 % Allowed : 10.21 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.16), residues: 2456 helix: -0.98 (0.13), residues: 1564 sheet: -2.51 (0.39), residues: 108 loop : -2.64 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 327 TYR 0.016 0.001 TYR B 547 PHE 0.013 0.001 PHE C 316 TRP 0.007 0.001 TRP C 559 HIS 0.002 0.000 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00210 (21964) covalent geometry : angle 0.54782 (29484) hydrogen bonds : bond 0.03398 ( 798) hydrogen bonds : angle 3.76874 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.844 Fit side-chains REVERT: A 159 MET cc_start: 0.7677 (mmm) cc_final: 0.7469 (mmm) REVERT: A 650 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4210 (m-80) REVERT: A 725 ASP cc_start: 0.7783 (t0) cc_final: 0.7541 (t0) REVERT: B 122 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8465 (ttp80) REVERT: B 159 MET cc_start: 0.7883 (mmm) cc_final: 0.7448 (mmm) REVERT: B 211 GLU cc_start: 0.7758 (pm20) cc_final: 0.7406 (pm20) REVERT: B 650 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4226 (m-80) REVERT: B 726 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 211 GLU cc_start: 0.7753 (pm20) cc_final: 0.7410 (pm20) REVERT: C 581 LYS cc_start: 0.6851 (mmtt) cc_final: 0.6636 (mptt) REVERT: C 603 VAL cc_start: 0.7484 (t) cc_final: 0.7157 (p) REVERT: C 650 TYR cc_start: 0.5220 (OUTLIER) cc_final: 0.4400 (m-80) REVERT: C 725 ASP cc_start: 0.7702 (t0) cc_final: 0.7472 (t0) REVERT: D 544 TYR cc_start: 0.6172 (m-80) cc_final: 0.5964 (m-80) REVERT: D 603 VAL cc_start: 0.7405 (t) cc_final: 0.7135 (p) REVERT: D 650 TYR cc_start: 0.5063 (OUTLIER) cc_final: 0.4396 (m-80) outliers start: 47 outliers final: 24 residues processed: 286 average time/residue: 0.1327 time to fit residues: 62.4559 Evaluate side-chains 247 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 255 GLN D 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111475 restraints weight = 32832.594| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.31 r_work: 0.3162 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21964 Z= 0.136 Angle : 0.586 8.964 29484 Z= 0.297 Chirality : 0.040 0.171 3232 Planarity : 0.003 0.042 3556 Dihedral : 18.633 102.269 3812 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.94 % Favored : 93.73 % Rotamer: Outliers : 2.13 % Allowed : 10.48 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2456 helix: -0.69 (0.13), residues: 1556 sheet: -2.22 (0.41), residues: 108 loop : -2.56 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 327 TYR 0.016 0.001 TYR B 460 PHE 0.014 0.001 PHE D 316 TRP 0.007 0.001 TRP C 559 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00319 (21964) covalent geometry : angle 0.58566 (29484) hydrogen bonds : bond 0.04079 ( 798) hydrogen bonds : angle 3.85539 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.819 Fit side-chains REVERT: A 159 MET cc_start: 0.7685 (mmm) cc_final: 0.7478 (mmm) REVERT: A 544 TYR cc_start: 0.6232 (m-80) cc_final: 0.5972 (m-80) REVERT: A 650 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.4252 (m-80) REVERT: B 122 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8478 (ttp80) REVERT: B 211 GLU cc_start: 0.7782 (pm20) cc_final: 0.7440 (pm20) REVERT: B 544 TYR cc_start: 0.6268 (m-80) cc_final: 0.6026 (m-80) REVERT: B 650 TYR cc_start: 0.5150 (OUTLIER) cc_final: 0.4265 (m-80) REVERT: B 726 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 122 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8449 (ttp80) REVERT: C 211 GLU cc_start: 0.7728 (pm20) cc_final: 0.7408 (pm20) REVERT: C 544 TYR cc_start: 0.6307 (m-80) cc_final: 0.6054 (m-80) REVERT: C 581 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6861 (mptt) REVERT: C 603 VAL cc_start: 0.7472 (t) cc_final: 0.7121 (p) REVERT: C 650 TYR cc_start: 0.5339 (OUTLIER) cc_final: 0.4400 (m-80) REVERT: D 603 VAL cc_start: 0.7487 (t) cc_final: 0.7184 (p) REVERT: D 650 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4441 (m-80) outliers start: 47 outliers final: 34 residues processed: 264 average time/residue: 0.1369 time to fit residues: 58.8130 Evaluate side-chains 254 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 255 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN D 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116989 restraints weight = 32746.123| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.24 r_work: 0.3240 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21964 Z= 0.092 Angle : 0.530 10.157 29484 Z= 0.269 Chirality : 0.038 0.165 3232 Planarity : 0.003 0.041 3556 Dihedral : 17.868 100.338 3812 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 2.00 % Allowed : 11.30 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2456 helix: -0.31 (0.13), residues: 1600 sheet: -1.75 (0.44), residues: 108 loop : -2.55 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 327 TYR 0.017 0.001 TYR C 547 PHE 0.012 0.001 PHE A 316 TRP 0.007 0.001 TRP B 559 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00197 (21964) covalent geometry : angle 0.53011 (29484) hydrogen bonds : bond 0.03110 ( 798) hydrogen bonds : angle 3.60499 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.820 Fit side-chains REVERT: A 159 MET cc_start: 0.7694 (mmm) cc_final: 0.7488 (mmm) REVERT: A 529 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: A 544 TYR cc_start: 0.6104 (m-80) cc_final: 0.5893 (m-80) REVERT: A 650 TYR cc_start: 0.4773 (OUTLIER) cc_final: 0.3959 (m-80) REVERT: B 122 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8505 (ttp80) REVERT: B 211 GLU cc_start: 0.7686 (pm20) cc_final: 0.7419 (pm20) REVERT: B 544 TYR cc_start: 0.6115 (m-80) cc_final: 0.5886 (m-80) REVERT: B 650 TYR cc_start: 0.4807 (OUTLIER) cc_final: 0.3915 (m-80) REVERT: B 726 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 122 ARG cc_start: 0.8703 (ttm170) cc_final: 0.8471 (ttp80) REVERT: C 159 MET cc_start: 0.7838 (mmm) cc_final: 0.7587 (mmm) REVERT: C 211 GLU cc_start: 0.7651 (pm20) cc_final: 0.7376 (pm20) REVERT: C 529 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: C 544 TYR cc_start: 0.6068 (m-80) cc_final: 0.5837 (m-80) REVERT: C 603 VAL cc_start: 0.7455 (t) cc_final: 0.7085 (p) REVERT: C 650 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4062 (m-80) REVERT: D 603 VAL cc_start: 0.7466 (t) cc_final: 0.7150 (p) REVERT: D 650 TYR cc_start: 0.5036 (OUTLIER) cc_final: 0.4297 (m-80) outliers start: 44 outliers final: 27 residues processed: 257 average time/residue: 0.1348 time to fit residues: 56.3441 Evaluate side-chains 240 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 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 = 0.3939 r_free = 0.3939 target = 0.152749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117657 restraints weight = 32621.481| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.07 r_work: 0.3281 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21964 Z= 0.089 Angle : 0.523 8.449 29484 Z= 0.265 Chirality : 0.038 0.166 3232 Planarity : 0.003 0.040 3556 Dihedral : 17.243 96.490 3812 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.72 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2456 helix: 0.17 (0.13), residues: 1560 sheet: -1.36 (0.46), residues: 108 loop : -2.42 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.010 0.001 TYR D 460 PHE 0.012 0.001 PHE D 316 TRP 0.007 0.001 TRP A 559 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00189 (21964) covalent geometry : angle 0.52301 (29484) hydrogen bonds : bond 0.03040 ( 798) hydrogen bonds : angle 3.59652 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.784 Fit side-chains REVERT: A 529 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6719 (tt0) REVERT: A 544 TYR cc_start: 0.6035 (m-80) cc_final: 0.5772 (m-80) REVERT: A 650 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.3831 (m-80) REVERT: B 159 MET cc_start: 0.7885 (mmm) cc_final: 0.7629 (mmm) REVERT: B 211 GLU cc_start: 0.8033 (pm20) cc_final: 0.7713 (pm20) REVERT: B 544 TYR cc_start: 0.6051 (m-80) cc_final: 0.5831 (m-80) REVERT: B 650 TYR cc_start: 0.4818 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: B 726 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 122 ARG cc_start: 0.8749 (ttm170) cc_final: 0.8536 (ttp80) REVERT: C 159 MET cc_start: 0.7873 (mmm) cc_final: 0.7635 (mmm) REVERT: C 211 GLU cc_start: 0.8000 (pm20) cc_final: 0.7679 (pm20) REVERT: C 529 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: C 544 TYR cc_start: 0.5922 (m-80) cc_final: 0.5722 (m-80) REVERT: C 603 VAL cc_start: 0.7497 (t) cc_final: 0.7111 (p) REVERT: C 650 TYR cc_start: 0.4744 (OUTLIER) cc_final: 0.3876 (m-80) REVERT: D 603 VAL cc_start: 0.7531 (t) cc_final: 0.7169 (p) REVERT: D 650 TYR cc_start: 0.4904 (OUTLIER) cc_final: 0.4195 (m-80) outliers start: 38 outliers final: 22 residues processed: 263 average time/residue: 0.1353 time to fit residues: 57.2726 Evaluate side-chains 242 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 230 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 164 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111201 restraints weight = 32678.074| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.24 r_work: 0.3175 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21964 Z= 0.136 Angle : 0.579 8.685 29484 Z= 0.292 Chirality : 0.040 0.176 3232 Planarity : 0.003 0.040 3556 Dihedral : 17.360 98.391 3812 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 1.59 % Allowed : 11.98 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2456 helix: 0.15 (0.13), residues: 1540 sheet: -1.33 (0.46), residues: 108 loop : -2.39 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.021 0.001 TYR B 460 PHE 0.015 0.001 PHE D 316 TRP 0.008 0.001 TRP C 559 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00324 (21964) covalent geometry : angle 0.57885 (29484) hydrogen bonds : bond 0.03852 ( 798) hydrogen bonds : angle 3.80065 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.827 Fit side-chains REVERT: A 529 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: A 544 TYR cc_start: 0.6142 (m-80) cc_final: 0.5897 (m-80) REVERT: A 650 TYR cc_start: 0.4732 (OUTLIER) cc_final: 0.3771 (m-80) REVERT: B 211 GLU cc_start: 0.8104 (pm20) cc_final: 0.7740 (pm20) REVERT: B 544 TYR cc_start: 0.6141 (m-80) cc_final: 0.5936 (m-80) REVERT: B 650 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.3830 (m-80) REVERT: B 726 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 122 ARG cc_start: 0.8763 (ttm170) cc_final: 0.8527 (ttp80) REVERT: C 159 MET cc_start: 0.7898 (mmm) cc_final: 0.7624 (mmm) REVERT: C 211 GLU cc_start: 0.8079 (pm20) cc_final: 0.7720 (pm20) REVERT: C 529 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: C 544 TYR cc_start: 0.6030 (m-80) cc_final: 0.5785 (m-80) REVERT: C 603 VAL cc_start: 0.7498 (t) cc_final: 0.7104 (p) REVERT: C 650 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.3922 (m-80) REVERT: D 603 VAL cc_start: 0.7536 (t) cc_final: 0.7171 (p) REVERT: D 650 TYR cc_start: 0.4896 (OUTLIER) cc_final: 0.4166 (m-80) outliers start: 35 outliers final: 26 residues processed: 252 average time/residue: 0.1410 time to fit residues: 56.8588 Evaluate side-chains 249 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 98 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 218 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 145 optimal weight: 0.0470 chunk 166 optimal weight: 10.0000 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 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 = 0.3928 r_free = 0.3928 target = 0.151852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116606 restraints weight = 32720.072| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.04 r_work: 0.3268 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21964 Z= 0.093 Angle : 0.530 8.607 29484 Z= 0.269 Chirality : 0.038 0.179 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.858 94.681 3812 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.54 % Allowed : 12.02 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.67 (0.17), residues: 2456 helix: 0.53 (0.13), residues: 1540 sheet: -1.30 (0.45), residues: 112 loop : -2.21 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.016 0.001 TYR A 460 PHE 0.013 0.001 PHE B 316 TRP 0.006 0.001 TRP C 559 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00202 (21964) covalent geometry : angle 0.53048 (29484) hydrogen bonds : bond 0.03023 ( 798) hydrogen bonds : angle 3.65906 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.690 Fit side-chains REVERT: A 529 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: A 531 VAL cc_start: 0.8705 (t) cc_final: 0.8444 (m) REVERT: A 650 TYR cc_start: 0.4592 (OUTLIER) cc_final: 0.3636 (m-80) REVERT: B 211 GLU cc_start: 0.8045 (pm20) cc_final: 0.7729 (pm20) REVERT: B 531 VAL cc_start: 0.8705 (t) cc_final: 0.8435 (m) REVERT: B 650 TYR cc_start: 0.4446 (OUTLIER) cc_final: 0.3517 (m-80) REVERT: B 726 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 122 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8567 (ttp80) REVERT: C 159 MET cc_start: 0.7911 (mmm) cc_final: 0.7650 (mmm) REVERT: C 211 GLU cc_start: 0.8015 (pm20) cc_final: 0.7697 (pm20) REVERT: C 529 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: C 531 VAL cc_start: 0.8737 (t) cc_final: 0.8517 (m) REVERT: C 603 VAL cc_start: 0.7485 (t) cc_final: 0.7058 (p) REVERT: C 650 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.3771 (m-80) REVERT: D 603 VAL cc_start: 0.7499 (t) cc_final: 0.7109 (p) REVERT: D 650 TYR cc_start: 0.4737 (OUTLIER) cc_final: 0.4102 (m-80) outliers start: 34 outliers final: 26 residues processed: 257 average time/residue: 0.1326 time to fit residues: 54.6404 Evaluate side-chains 254 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 237 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 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 = 0.3938 r_free = 0.3938 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117258 restraints weight = 32710.881| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.07 r_work: 0.3279 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21964 Z= 0.091 Angle : 0.527 8.457 29484 Z= 0.267 Chirality : 0.038 0.178 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.560 89.236 3812 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.41 % Allowed : 12.25 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.17), residues: 2456 helix: 0.68 (0.13), residues: 1540 sheet: -1.01 (0.46), residues: 108 loop : -2.17 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.021 0.001 TYR C 460 PHE 0.013 0.001 PHE D 316 TRP 0.007 0.001 TRP B 559 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00195 (21964) covalent geometry : angle 0.52701 (29484) hydrogen bonds : bond 0.02987 ( 798) hydrogen bonds : angle 3.63537 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.733 Fit side-chains REVERT: A 529 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: A 531 VAL cc_start: 0.8728 (t) cc_final: 0.8455 (m) REVERT: A 650 TYR cc_start: 0.4514 (OUTLIER) cc_final: 0.3570 (m-80) REVERT: B 159 MET cc_start: 0.7902 (mmm) cc_final: 0.7514 (mmm) REVERT: B 211 GLU cc_start: 0.8019 (pm20) cc_final: 0.7703 (pm20) REVERT: B 650 TYR cc_start: 0.4347 (OUTLIER) cc_final: 0.3432 (m-80) REVERT: B 726 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 122 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8568 (ttp80) REVERT: C 159 MET cc_start: 0.7918 (mmm) cc_final: 0.7622 (mmm) REVERT: C 211 GLU cc_start: 0.7999 (pm20) cc_final: 0.7682 (pm20) REVERT: C 529 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: C 540 TYR cc_start: 0.8373 (t80) cc_final: 0.7734 (t80) REVERT: C 650 TYR cc_start: 0.4609 (OUTLIER) cc_final: 0.3727 (m-80) REVERT: D 603 VAL cc_start: 0.7538 (t) cc_final: 0.7103 (p) REVERT: D 650 TYR cc_start: 0.4612 (OUTLIER) cc_final: 0.4093 (m-80) outliers start: 31 outliers final: 22 residues processed: 254 average time/residue: 0.1410 time to fit residues: 57.5616 Evaluate side-chains 248 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 161 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112606 restraints weight = 32713.704| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.18 r_work: 0.3207 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21964 Z= 0.110 Angle : 0.554 8.500 29484 Z= 0.280 Chirality : 0.039 0.190 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.597 87.036 3812 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.36 % Allowed : 12.61 % Favored : 86.03 % 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: -0.64 (0.17), residues: 2456 helix: 0.53 (0.13), residues: 1572 sheet: -1.01 (0.47), residues: 108 loop : -2.29 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.016 0.001 TYR C 460 PHE 0.016 0.001 PHE C 316 TRP 0.008 0.001 TRP C 559 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00253 (21964) covalent geometry : angle 0.55371 (29484) hydrogen bonds : bond 0.03481 ( 798) hydrogen bonds : angle 3.72597 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.13 seconds wall clock time: 100 minutes 14.52 seconds (6014.52 seconds total)