Starting phenix.real_space_refine on Sat Jul 4 15:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugg_26488/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugg_26488/07_2026/7ugg_26488.map" } 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-6108/lib/python3.11/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: 5.33, per 1000 atoms: 0.25 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: 1.93 Conformation dependent library (CDL) restraints added in 932.1 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: 0.62 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: 3.50 Time building geometry restraints manager: 2.52 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: 12736 35.74 - 71.47: 422 71.47 - 107.21: 62 107.21 - 142.94: 28 142.94 - 178.68: 8 Dihedral angle restraints: 13256 sinusoidal: 5948 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 13253 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.720 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 18.695 178.679 8512 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/Z covalent geometry : bond 0.01202 / 0.56 (21964) covalent geometry : angle 1.44510 / 0.70 (29484) hydrogen bonds : bond 0.37209 / 24.22 ( 798) hydrogen bonds : angle 10.49589 / 7.10 ( 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 : 0.837 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: 0.1495 time to fit residues: 99.3980 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 : 0.725 ------------------------------------------------------------------------------- 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... A 140 GLN 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 140 GLN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.149792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111473 restraints weight = 32969.170| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.33 r_work: 0.3176 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 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 = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2468 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= 0.146 Angle : 0.654 8.662 29484 Z= 0.336 Chirality : 0.040 0.179 3232 Planarity : 0.005 0.048 3556 Dihedral : 21.930 160.892 3668 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.54 % Favored : 94.14 % Rotamer: Outliers : 2.04 % Allowed : 7.53 % Favored : 90.43 % 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 0.018 0.001 ARG B 716 TYR 0.017 0.002 TYR D 390 PHE 0.013 0.001 PHE C 316 TRP 0.013 0.002 TRP A 559 HIS 0.009 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (21964) covalent geometry : angle 0.65351 / 0.34 (29484) hydrogen bonds : bond 0.05366 / 3.51 ( 798) hydrogen bonds : angle 4.55638 / 3.11 ( 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 340 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.806 Fit side-chains REVERT: A 544 TYR cc_start: 0.6468 (m-80) cc_final: 0.6185 (m-80) REVERT: A 570 GLN cc_start: 0.8056 (tt0) cc_final: 0.7775 (tt0) REVERT: A 581 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6643 (mptt) REVERT: A 650 TYR cc_start: 0.5861 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: B 159 MET cc_start: 0.7857 (mmp) cc_final: 0.7627 (mmm) REVERT: B 211 GLU cc_start: 0.7879 (pm20) cc_final: 0.7568 (pm20) REVERT: B 544 TYR cc_start: 0.6548 (m-80) cc_final: 0.6237 (m-80) REVERT: B 570 GLN cc_start: 0.7976 (tt0) cc_final: 0.7697 (tt0) REVERT: B 581 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6891 (mptt) REVERT: B 726 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 531 VAL cc_start: 0.8608 (t) cc_final: 0.8296 (m) REVERT: C 544 TYR cc_start: 0.6531 (m-80) cc_final: 0.6217 (m-80) REVERT: C 570 GLN cc_start: 0.7936 (tt0) cc_final: 0.7637 (tt0) REVERT: C 581 LYS cc_start: 0.7096 (mmtt) cc_final: 0.6874 (mptt) REVERT: D 544 TYR cc_start: 0.6281 (m-80) cc_final: 0.5912 (m-80) REVERT: D 570 GLN cc_start: 0.8253 (tt0) cc_final: 0.7910 (tt0) REVERT: D 650 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5054 (m-10) outliers start: 45 outliers final: 14 residues processed: 330 average time/residue: 0.1489 time to fit residues: 77.7281 Evaluate side-chains 261 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 A residue 685 SER 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 B residue 685 SER 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: 3.9990 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112746 restraints weight = 32753.030| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.21 r_work: 0.3191 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21964 Z= 0.135 Angle : 0.609 8.653 29484 Z= 0.308 Chirality : 0.040 0.171 3232 Planarity : 0.004 0.045 3556 Dihedral : 19.817 120.752 3668 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.86 % Favored : 93.81 % Rotamer: Outliers : 1.72 % Allowed : 8.71 % Favored : 89.56 % 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: -3.13 (0.15), residues: 2456 helix: -1.58 (0.12), residues: 1512 sheet: -3.33 (0.33), residues: 112 loop : -2.57 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.017 0.002 TYR B 390 PHE 0.014 0.001 PHE B 316 TRP 0.008 0.001 TRP B 559 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21964) covalent geometry : angle 0.60877 / 0.31 (29484) hydrogen bonds : bond 0.04591 / 3.02 ( 798) hydrogen bonds : angle 4.08331 / 2.80 ( 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 303 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.839 Fit side-chains REVERT: A 531 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8447 (m) REVERT: A 544 TYR cc_start: 0.6386 (m-80) cc_final: 0.6132 (m-80) REVERT: A 581 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6648 (mptt) REVERT: A 650 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5177 (m-80) REVERT: B 211 GLU cc_start: 0.8137 (pm20) cc_final: 0.7692 (pm20) REVERT: B 531 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8393 (m) REVERT: B 544 TYR cc_start: 0.6425 (m-80) cc_final: 0.6179 (m-80) REVERT: B 650 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5159 (m-80) REVERT: B 653 LEU cc_start: 0.5507 (tt) cc_final: 0.4930 (mm) REVERT: B 726 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 211 GLU cc_start: 0.8063 (pm20) cc_final: 0.7630 (pm20) REVERT: C 540 TYR cc_start: 0.8410 (t80) cc_final: 0.7872 (t80) REVERT: C 544 TYR cc_start: 0.6363 (m-80) cc_final: 0.6116 (m-80) REVERT: C 581 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6804 (mptt) REVERT: C 650 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: C 653 LEU cc_start: 0.5366 (tt) cc_final: 0.5134 (mm) REVERT: D 544 TYR cc_start: 0.6276 (m-80) cc_final: 0.5982 (m-80) REVERT: D 581 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6650 (mptt) REVERT: D 650 TYR cc_start: 0.5558 (OUTLIER) cc_final: 0.4940 (m-80) outliers start: 38 outliers final: 19 residues processed: 293 average time/residue: 0.1455 time to fit residues: 68.3752 Evaluate side-chains 252 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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 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 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: 9.9990 chunk 228 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN B 695 GLN D 227 GLN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108088 restraints weight = 33114.394| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.41 r_work: 0.3108 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21964 Z= 0.211 Angle : 0.670 7.866 29484 Z= 0.339 Chirality : 0.043 0.182 3232 Planarity : 0.004 0.050 3556 Dihedral : 19.071 116.129 3668 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.76 % Favored : 92.92 % Rotamer: Outliers : 3.04 % Allowed : 9.17 % Favored : 87.79 % 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: -2.70 (0.16), residues: 2456 helix: -1.22 (0.12), residues: 1540 sheet: -2.65 (0.39), residues: 108 loop : -2.55 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 319 TYR 0.018 0.002 TYR B 451 PHE 0.015 0.002 PHE D 316 TRP 0.007 0.001 TRP C 692 HIS 0.008 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (21964) covalent geometry : angle 0.67030 / 0.34 (29484) hydrogen bonds : bond 0.05240 / 3.44 ( 798) hydrogen bonds : angle 4.21906 / 2.90 ( 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 316 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 0.812 Fit side-chains REVERT: A 544 TYR cc_start: 0.6413 (m-80) cc_final: 0.6195 (m-80) REVERT: A 581 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6941 (mptt) REVERT: A 650 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.4751 (m-80) REVERT: A 725 ASP cc_start: 0.7786 (t0) cc_final: 0.7486 (t0) REVERT: B 122 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8432 (ttp80) REVERT: B 211 GLU cc_start: 0.7854 (pm20) cc_final: 0.7476 (pm20) REVERT: B 544 TYR cc_start: 0.6419 (m-80) cc_final: 0.6202 (m-80) REVERT: B 650 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.4753 (m-80) REVERT: B 726 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7884 (mm-30) REVERT: C 211 GLU cc_start: 0.7852 (pm20) cc_final: 0.7467 (pm20) REVERT: C 581 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6887 (mptt) REVERT: C 603 VAL cc_start: 0.7541 (t) cc_final: 0.7201 (p) REVERT: C 650 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: C 725 ASP cc_start: 0.7750 (t0) cc_final: 0.7451 (t0) REVERT: D 122 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8435 (ttp80) REVERT: D 544 TYR cc_start: 0.6377 (m-80) cc_final: 0.6089 (m-80) REVERT: D 581 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6744 (mptt) REVERT: D 603 VAL cc_start: 0.7531 (t) cc_final: 0.7227 (p) REVERT: D 650 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.4741 (m-80) outliers start: 67 outliers final: 45 residues processed: 298 average time/residue: 0.1447 time to fit residues: 69.4314 Evaluate side-chains 282 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 499 VAL Chi-restraints excluded: chain A residue 531 VAL 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 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 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 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 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 531 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 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 499 VAL Chi-restraints excluded: chain D residue 531 VAL 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 Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 255 GLN B 227 GLN B 255 GLN C 227 GLN C 255 GLN D 255 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111084 restraints weight = 32793.761| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.14 r_work: 0.3190 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21964 Z= 0.144 Angle : 0.595 10.004 29484 Z= 0.302 Chirality : 0.040 0.177 3232 Planarity : 0.003 0.047 3556 Dihedral : 18.226 110.452 3668 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.42 % Favored : 94.26 % Rotamer: Outliers : 2.22 % Allowed : 10.75 % 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: -2.26 (0.16), residues: 2456 helix: -0.87 (0.13), residues: 1568 sheet: -2.17 (0.43), residues: 108 loop : -2.49 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.013 0.001 TYR A 451 PHE 0.014 0.001 PHE B 316 TRP 0.008 0.001 TRP B 559 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (21964) covalent geometry : angle 0.59455 / 0.30 (29484) hydrogen bonds : bond 0.04159 / 2.74 ( 798) hydrogen bonds : angle 3.95384 / 2.71 ( 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 277 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.761 Fit side-chains REVERT: A 122 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8470 (ttp80) REVERT: A 529 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: A 581 LYS cc_start: 0.7052 (mmtt) cc_final: 0.6819 (mptt) REVERT: A 650 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: B 122 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8436 (ttp80) REVERT: B 211 GLU cc_start: 0.8023 (pm20) cc_final: 0.7631 (pm20) REVERT: B 650 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4263 (m-80) REVERT: B 726 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7953 (mm-30) REVERT: C 122 ARG cc_start: 0.8750 (ttm170) cc_final: 0.8419 (ttp80) REVERT: C 211 GLU cc_start: 0.7994 (pm20) cc_final: 0.7604 (pm20) REVERT: C 529 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: C 544 TYR cc_start: 0.6187 (m-80) cc_final: 0.5923 (m-80) REVERT: C 581 LYS cc_start: 0.7080 (mmtt) cc_final: 0.6823 (mptt) REVERT: C 603 VAL cc_start: 0.7618 (t) cc_final: 0.7260 (p) REVERT: C 650 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: D 122 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8468 (ttp80) REVERT: D 544 TYR cc_start: 0.6238 (m-80) cc_final: 0.5995 (m-80) REVERT: D 581 LYS cc_start: 0.7073 (mmtt) cc_final: 0.6867 (mptt) REVERT: D 603 VAL cc_start: 0.7569 (t) cc_final: 0.7242 (p) REVERT: D 650 TYR cc_start: 0.5342 (OUTLIER) cc_final: 0.4686 (m-80) outliers start: 49 outliers final: 37 residues processed: 266 average time/residue: 0.1517 time to fit residues: 64.1634 Evaluate side-chains 261 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 529 GLN Chi-restraints excluded: chain A residue 531 VAL 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 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 282 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 499 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 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 499 VAL Chi-restraints excluded: chain C residue 529 GLN 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 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 217 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.3935 r_free = 0.3935 target = 0.152290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116265 restraints weight = 32797.416| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.34 r_work: 0.3230 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21964 Z= 0.090 Angle : 0.530 9.242 29484 Z= 0.269 Chirality : 0.038 0.163 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.874 96.464 3668 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 1.54 % Allowed : 11.98 % Favored : 86.48 % 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: -1.52 (0.16), residues: 2456 helix: -0.21 (0.13), residues: 1556 sheet: -1.88 (0.44), residues: 112 loop : -2.37 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.018 0.001 TYR C 460 PHE 0.013 0.001 PHE B 316 TRP 0.007 0.001 TRP A 739 HIS 0.002 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (21964) covalent geometry : angle 0.52986 / 0.27 (29484) hydrogen bonds : bond 0.02981 / 1.98 ( 798) hydrogen bonds : angle 3.61835 / 2.49 ( 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 272 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8584 (ttp80) REVERT: A 529 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: A 544 TYR cc_start: 0.6202 (m-80) cc_final: 0.5958 (m-80) REVERT: A 581 LYS cc_start: 0.6826 (mmtt) cc_final: 0.6615 (mptt) REVERT: A 650 TYR cc_start: 0.4725 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: B 159 MET cc_start: 0.7864 (mmm) cc_final: 0.7495 (mmm) REVERT: B 211 GLU cc_start: 0.7705 (pm20) cc_final: 0.7412 (pm20) REVERT: B 514 GLN cc_start: 0.5026 (tp40) cc_final: 0.4501 (mm-40) REVERT: B 650 TYR cc_start: 0.4675 (OUTLIER) cc_final: 0.3782 (m-80) REVERT: B 726 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 122 ARG cc_start: 0.8727 (ttm170) cc_final: 0.8457 (ttp80) REVERT: C 159 MET cc_start: 0.7878 (mmm) cc_final: 0.7520 (mmm) REVERT: C 211 GLU cc_start: 0.7698 (pm20) cc_final: 0.7397 (pm20) REVERT: C 529 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6320 (tt0) REVERT: C 544 TYR cc_start: 0.6081 (m-80) cc_final: 0.5877 (m-80) REVERT: C 581 LYS cc_start: 0.6974 (mmtt) cc_final: 0.6632 (mptt) REVERT: C 603 VAL cc_start: 0.7408 (t) cc_final: 0.7025 (p) REVERT: C 650 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4233 (m-80) REVERT: D 544 TYR cc_start: 0.5976 (m-80) cc_final: 0.5536 (m-80) REVERT: D 603 VAL cc_start: 0.7476 (t) cc_final: 0.7115 (p) REVERT: D 650 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.4171 (m-80) outliers start: 34 outliers final: 16 residues processed: 262 average time/residue: 0.1428 time to fit residues: 60.4582 Evaluate side-chains 228 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 241 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR 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 241 VAL Chi-restraints excluded: chain D residue 531 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 0.0000 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 204 optimal weight: 0.0870 chunk 181 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114199 restraints weight = 32657.582| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.38 r_work: 0.3200 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3882 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= 0.102 Angle : 0.550 9.407 29484 Z= 0.277 Chirality : 0.039 0.172 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.608 91.922 3668 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 1.45 % Allowed : 11.93 % Favored : 86.62 % 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: -1.42 (0.17), residues: 2456 helix: -0.14 (0.13), residues: 1596 sheet: -1.41 (0.45), residues: 108 loop : -2.49 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 188 TYR 0.019 0.001 TYR B 460 PHE 0.015 0.001 PHE D 316 TRP 0.008 0.001 TRP B 559 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (21964) covalent geometry : angle 0.54996 / 0.28 (29484) hydrogen bonds : bond 0.03348 / 2.22 ( 798) hydrogen bonds : angle 3.64760 / 2.51 ( 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 261 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.881 Fit side-chains REVERT: A 122 ARG cc_start: 0.8791 (ttm170) cc_final: 0.8582 (ttp80) REVERT: A 529 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: A 544 TYR cc_start: 0.6209 (m-80) cc_final: 0.5878 (m-80) REVERT: A 581 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6785 (mptt) REVERT: A 650 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.3890 (m-80) REVERT: B 159 MET cc_start: 0.7852 (mmm) cc_final: 0.7458 (mmm) REVERT: B 211 GLU cc_start: 0.7765 (pm20) cc_final: 0.7478 (pm20) REVERT: B 650 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.3916 (m-80) REVERT: B 726 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 122 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8497 (ttp80) REVERT: C 159 MET cc_start: 0.7925 (mmm) cc_final: 0.7556 (mmm) REVERT: C 211 GLU cc_start: 0.7747 (pm20) cc_final: 0.7434 (pm20) REVERT: C 529 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6310 (tt0) REVERT: C 544 TYR cc_start: 0.6041 (m-80) cc_final: 0.5787 (m-80) REVERT: C 581 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6723 (mptt) REVERT: C 603 VAL cc_start: 0.7407 (t) cc_final: 0.7028 (p) REVERT: C 650 TYR cc_start: 0.4990 (OUTLIER) cc_final: 0.4178 (m-80) REVERT: D 122 ARG cc_start: 0.8896 (ttp80) cc_final: 0.8656 (ttp80) REVERT: D 278 VAL cc_start: 0.8953 (t) cc_final: 0.8743 (t) REVERT: D 603 VAL cc_start: 0.7462 (t) cc_final: 0.7104 (p) REVERT: D 650 TYR cc_start: 0.4856 (OUTLIER) cc_final: 0.4148 (m-80) outliers start: 32 outliers final: 19 residues processed: 255 average time/residue: 0.1467 time to fit residues: 60.3336 Evaluate side-chains 239 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 323 MET 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 241 VAL 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 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 531 VAL 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 127 VAL 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 641 ASP 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: 0.7980 chunk 187 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.3886 r_free = 0.3886 target = 0.148295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111383 restraints weight = 32635.769| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.41 r_work: 0.3153 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21964 Z= 0.144 Angle : 0.601 8.639 29484 Z= 0.303 Chirality : 0.041 0.183 3232 Planarity : 0.003 0.040 3556 Dihedral : 16.755 90.276 3668 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 1.45 % Allowed : 12.25 % Favored : 86.30 % 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: -1.39 (0.16), residues: 2456 helix: -0.11 (0.13), residues: 1560 sheet: -1.25 (0.46), residues: 108 loop : -2.43 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.016 0.002 TYR B 460 PHE 0.015 0.001 PHE C 316 TRP 0.009 0.001 TRP C 559 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (21964) covalent geometry : angle 0.60121 / 0.30 (29484) hydrogen bonds : bond 0.04108 / 2.71 ( 798) hydrogen bonds : angle 3.89284 / 2.68 ( 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 248 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.850 Fit side-chains REVERT: A 122 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8515 (ttp80) REVERT: A 529 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: A 544 TYR cc_start: 0.6193 (m-80) cc_final: 0.5987 (m-80) REVERT: A 581 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6819 (mptt) REVERT: A 650 TYR cc_start: 0.4740 (OUTLIER) cc_final: 0.3842 (m-80) REVERT: B 159 MET cc_start: 0.7836 (mmm) cc_final: 0.7355 (mmm) REVERT: B 211 GLU cc_start: 0.7795 (pm20) cc_final: 0.7499 (pm20) REVERT: B 650 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.3956 (m-80) REVERT: B 726 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 122 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8462 (ttp80) REVERT: C 159 MET cc_start: 0.7976 (mmm) cc_final: 0.7554 (mmm) REVERT: C 211 GLU cc_start: 0.7766 (pm20) cc_final: 0.7464 (pm20) REVERT: C 529 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: C 544 TYR cc_start: 0.6199 (m-80) cc_final: 0.5939 (m-80) REVERT: C 581 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6789 (mptt) REVERT: D 650 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4343 (m-80) outliers start: 32 outliers final: 24 residues processed: 242 average time/residue: 0.1463 time to fit residues: 56.9487 Evaluate side-chains 242 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 529 GLN Chi-restraints excluded: chain A residue 540 TYR 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 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL 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 531 VAL Chi-restraints excluded: chain C residue 605 LEU 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 531 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 98 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.3913 r_free = 0.3913 target = 0.150461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113753 restraints weight = 32779.333| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.14 r_work: 0.3233 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21964 Z= 0.103 Angle : 0.558 9.018 29484 Z= 0.283 Chirality : 0.039 0.176 3232 Planarity : 0.003 0.042 3556 Dihedral : 16.292 88.745 3668 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 1.68 % Allowed : 12.25 % Favored : 86.07 % 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: -1.03 (0.17), residues: 2456 helix: 0.14 (0.13), residues: 1572 sheet: -1.04 (0.47), residues: 108 loop : -2.27 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.015 0.001 TYR D 460 PHE 0.014 0.001 PHE C 316 TRP 0.007 0.001 TRP B 559 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (21964) covalent geometry : angle 0.55792 / 0.28 (29484) hydrogen bonds : bond 0.03383 / 2.23 ( 798) hydrogen bonds : angle 3.70338 / 2.54 ( 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 259 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.917 Fit side-chains REVERT: A 122 ARG cc_start: 0.8789 (ttm170) cc_final: 0.8541 (ttp80) REVERT: A 529 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6714 (tt0) REVERT: A 544 TYR cc_start: 0.6102 (m-80) cc_final: 0.5876 (m-80) REVERT: A 581 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6751 (mptt) REVERT: A 650 TYR cc_start: 0.4658 (OUTLIER) cc_final: 0.3720 (m-80) REVERT: B 159 MET cc_start: 0.7826 (mmm) cc_final: 0.7380 (mmm) REVERT: B 211 GLU cc_start: 0.8025 (pm20) cc_final: 0.7681 (pm20) REVERT: B 650 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.3799 (m-80) REVERT: B 726 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8002 (mm-30) REVERT: C 122 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8498 (ttp80) REVERT: C 159 MET cc_start: 0.7972 (mmm) cc_final: 0.7576 (mmm) REVERT: C 211 GLU cc_start: 0.8024 (pm20) cc_final: 0.7686 (pm20) REVERT: C 529 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6594 (tt0) REVERT: C 544 TYR cc_start: 0.6076 (m-80) cc_final: 0.5819 (m-80) REVERT: D 650 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4161 (m-80) outliers start: 37 outliers final: 24 residues processed: 248 average time/residue: 0.1483 time to fit residues: 59.1747 Evaluate side-chains 247 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 529 GLN Chi-restraints excluded: chain A residue 540 TYR 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 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL 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 531 VAL Chi-restraints excluded: chain C residue 605 LEU 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 531 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 210 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.3891 r_free = 0.3891 target = 0.148766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112117 restraints weight = 32813.438| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.25 r_work: 0.3174 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4010 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= 0.127 Angle : 0.585 8.779 29484 Z= 0.296 Chirality : 0.040 0.180 3232 Planarity : 0.003 0.041 3556 Dihedral : 16.340 88.244 3668 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 1.41 % Allowed : 12.98 % Favored : 85.62 % 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: -0.98 (0.17), residues: 2456 helix: 0.25 (0.13), residues: 1528 sheet: -1.00 (0.47), residues: 108 loop : -2.28 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.023 0.001 TYR C 460 PHE 0.015 0.001 PHE C 316 TRP 0.008 0.001 TRP C 559 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21964) covalent geometry : angle 0.58511 / 0.30 (29484) hydrogen bonds : bond 0.03799 / 2.50 ( 798) hydrogen bonds : angle 3.85835 / 2.65 ( 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 : 0.860 Fit side-chains REVERT: A 122 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8518 (ttp80) REVERT: A 529 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: A 581 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6817 (mptt) REVERT: A 650 TYR cc_start: 0.4636 (OUTLIER) cc_final: 0.3776 (m-80) REVERT: B 159 MET cc_start: 0.7806 (mmm) cc_final: 0.7328 (mmm) REVERT: B 211 GLU cc_start: 0.7788 (pm20) cc_final: 0.7500 (pm20) REVERT: B 650 TYR cc_start: 0.4675 (OUTLIER) cc_final: 0.3862 (m-80) REVERT: B 726 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7779 (mm-30) REVERT: C 122 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8494 (ttp80) REVERT: C 159 MET cc_start: 0.7962 (mmm) cc_final: 0.7506 (mmm) REVERT: C 211 GLU cc_start: 0.7764 (pm20) cc_final: 0.7477 (pm20) REVERT: C 529 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: C 544 TYR cc_start: 0.6108 (m-80) cc_final: 0.5859 (m-80) REVERT: D 650 TYR cc_start: 0.4694 (OUTLIER) cc_final: 0.4085 (m-80) outliers start: 31 outliers final: 25 residues processed: 254 average time/residue: 0.1478 time to fit residues: 59.7844 Evaluate side-chains 251 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 529 GLN Chi-restraints excluded: chain A residue 540 TYR 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 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL 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 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 605 LEU 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 531 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 161 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3919 r_free = 0.3919 target = 0.151116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114428 restraints weight = 32832.664| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4191 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 : 0.552 8.600 29484 Z= 0.280 Chirality : 0.038 0.173 3232 Planarity : 0.003 0.041 3556 Dihedral : 15.867 87.040 3668 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.54 % Allowed : 12.89 % Favored : 85.57 % 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: -0.72 (0.17), residues: 2456 helix: 0.42 (0.14), residues: 1544 sheet: -0.89 (0.47), residues: 108 loop : -2.16 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.017 0.001 TYR C 460 PHE 0.012 0.001 PHE C 316 TRP 0.006 0.001 TRP B 739 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (21964) covalent geometry : angle 0.55153 / 0.28 (29484) hydrogen bonds : bond 0.03152 / 2.08 ( 798) hydrogen bonds : angle 3.73930 / 2.56 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5673.13 seconds wall clock time: 97 minutes 57.85 seconds (5877.85 seconds total)