Starting phenix.real_space_refine on Wed Jun 18 21:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugg_26488/06_2025/7ugg_26488.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.19, per 1000 atoms: 0.61 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: 5.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.15 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: 7.05 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3284 1.30 - 1.43: 5668 1.43 - 1.55: 12639 1.55 - 1.68: 177 1.68 - 1.81: 196 Bond restraints: 21964 Sorted by residual: bond pdb=" C09 N8R B 907 " pdb=" C10 N8R B 907 " ideal model delta sigma weight residual 1.377 1.539 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C09 N8R A 905 " pdb=" C10 N8R A 905 " ideal model delta sigma weight residual 1.377 1.539 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C09 N8R A 907 " pdb=" C10 N8R A 907 " ideal model delta sigma weight residual 1.377 1.538 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" C09 N8R D 907 " pdb=" C10 N8R D 907 " ideal model delta sigma weight residual 1.377 1.537 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C18 N8R A 907 " pdb=" N01 N8R A 907 " ideal model delta sigma weight residual 1.463 1.309 0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 21959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 28217 2.80 - 5.61: 906 5.61 - 8.41: 226 8.41 - 11.21: 89 11.21 - 14.02: 46 Bond angle restraints: 29484 Sorted by residual: angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" C VAL B 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL D 248 " pdb=" CA VAL D 248 " pdb=" C VAL D 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL C 248 " pdb=" CA VAL C 248 " pdb=" C VAL C 248 " ideal model delta sigma weight residual 112.96 106.37 6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 112.96 106.40 6.56 1.00e+00 1.00e+00 4.30e+01 angle pdb=" N GLY A 602 " pdb=" CA GLY A 602 " pdb=" C GLY A 602 " ideal model delta sigma weight residual 112.50 118.44 -5.94 1.16e+00 7.43e-01 2.62e+01 ... (remaining 29479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 12845 35.74 - 71.47: 457 71.47 - 107.21: 62 107.21 - 142.94: 28 142.94 - 178.68: 8 Dihedral angle restraints: 13400 sinusoidal: 6092 harmonic: 7308 Sorted by residual: dihedral pdb=" CA ASP B 315 " pdb=" C ASP B 315 " pdb=" N PHE B 316 " pdb=" CA PHE B 316 " ideal model delta harmonic sigma weight residual 180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP A 315 " pdb=" C ASP A 315 " pdb=" N PHE A 316 " pdb=" CA PHE A 316 " ideal model delta harmonic sigma weight residual -180.00 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP D 315 " pdb=" C ASP D 315 " pdb=" N PHE D 316 " pdb=" CA PHE D 316 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 13397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2769 0.073 - 0.146: 442 0.146 - 0.218: 17 0.218 - 0.291: 0 0.291 - 0.364: 4 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 475 " pdb=" CB LEU D 475 " pdb=" CD1 LEU D 475 " pdb=" CD2 LEU D 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU C 475 " pdb=" CB LEU C 475 " pdb=" CD1 LEU C 475 " pdb=" CD2 LEU C 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3229 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.11e+00 pdb=" CG PHE A 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE C 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 526 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 526 " -0.012 2.00e-02 2.50e+03 2.14e-02 7.98e+00 pdb=" CG PHE D 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 526 " -0.006 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2022 2.73 - 3.27: 19061 3.27 - 3.82: 31567 3.82 - 4.36: 40083 4.36 - 4.90: 69755 Nonbonded interactions: 162488 Sorted by model distance: nonbonded pdb=" OH TYR C 213 " pdb=" O PRO D 753 " model vdw 2.192 3.040 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR D 213 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO B 753 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 213 " pdb=" O PRO C 753 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 321 " pdb=" OE2 GLU A 334 " model vdw 2.304 3.040 ... (remaining 162483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'B' and (resid 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'C' and (resid 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'D' and (resid 118 through 756 or resid 901 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 48.560 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.162 21964 Z= 0.563 Angle : 1.445 14.018 29484 Z= 0.704 Chirality : 0.052 0.364 3232 Planarity : 0.007 0.064 3556 Dihedral : 18.879 178.679 8656 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.003 TRP C 493 HIS 0.008 0.002 HIS B 301 PHE 0.044 0.003 PHE A 526 TYR 0.024 0.004 TYR D 390 ARG 0.008 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.37209 ( 798) hydrogen bonds : angle 10.49589 ( 2322) covalent geometry : bond 0.01202 (21964) covalent geometry : angle 1.44510 (29484) *********************** 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 : 2.750 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: 0.5801 (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: 0.3897 time to fit residues: 258.9578 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 : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 178 ASN B 255 GLN B 477 HIS B 647 ASN B 671 ASN B 745 HIS C 178 ASN C 255 GLN C 477 HIS C 647 ASN C 671 ASN C 745 HIS D 143 GLN D 178 ASN D 255 GLN D 477 HIS D 745 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113488 restraints weight = 32880.559| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.31 r_work: 0.3207 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21964 Z= 0.127 Angle : 0.629 8.746 29484 Z= 0.322 Chirality : 0.040 0.167 3232 Planarity : 0.005 0.044 3556 Dihedral : 21.792 155.333 3812 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.50 % Favored : 94.18 % Rotamer: Outliers : 1.95 % Allowed : 7.67 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.13), residues: 2456 helix: -2.74 (0.10), residues: 1488 sheet: -3.73 (0.32), residues: 112 loop : -2.69 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 559 HIS 0.008 0.001 HIS A 471 PHE 0.012 0.001 PHE C 316 TYR 0.014 0.001 TYR D 390 ARG 0.002 0.000 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 798) hydrogen bonds : angle 4.50301 ( 2322) covalent geometry : bond 0.00276 (21964) covalent geometry : angle 0.62929 (29484) *********************** 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 337 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 3.154 Fit side-chains REVERT: A 544 TYR cc_start: 0.6446 (m-80) cc_final: 0.6170 (m-80) REVERT: A 570 GLN cc_start: 0.7820 (tt0) cc_final: 0.7583 (tt0) REVERT: A 581 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6788 (mptt) REVERT: A 650 TYR cc_start: 0.5732 (OUTLIER) cc_final: 0.5399 (m-80) REVERT: B 544 TYR cc_start: 0.6468 (m-80) cc_final: 0.6166 (m-80) REVERT: B 570 GLN cc_start: 0.7732 (tt0) cc_final: 0.7491 (tt0) REVERT: B 581 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6827 (mptt) REVERT: B 726 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 254 TYR cc_start: 0.7910 (m-10) cc_final: 0.7694 (m-10) REVERT: C 531 VAL cc_start: 0.8584 (t) cc_final: 0.8270 (m) REVERT: C 544 TYR cc_start: 0.6451 (m-80) cc_final: 0.6154 (m-80) REVERT: C 570 GLN cc_start: 0.7698 (tt0) cc_final: 0.7449 (tt0) REVERT: C 581 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6867 (mptt) REVERT: C 653 LEU cc_start: 0.5783 (tp) cc_final: 0.5161 (mp) REVERT: D 254 TYR cc_start: 0.7956 (m-80) cc_final: 0.7739 (m-10) REVERT: D 544 TYR cc_start: 0.6283 (m-80) cc_final: 0.5928 (m-80) REVERT: D 570 GLN cc_start: 0.8082 (tt0) cc_final: 0.7843 (tt0) REVERT: D 650 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.4878 (m-10) REVERT: D 716 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.7185 (mmt180) outliers start: 43 outliers final: 13 residues processed: 327 average time/residue: 0.3870 time to fit residues: 203.0922 Evaluate side-chains 255 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 695 GLN B 695 GLN D 643 ASN D 695 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.147911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110595 restraints weight = 32563.816| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.42 r_work: 0.3143 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21964 Z= 0.153 Angle : 0.629 8.491 29484 Z= 0.317 Chirality : 0.041 0.174 3232 Planarity : 0.004 0.043 3556 Dihedral : 20.042 117.982 3812 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.15 % Favored : 93.53 % Rotamer: Outliers : 2.00 % Allowed : 9.12 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.15), residues: 2456 helix: -1.60 (0.12), residues: 1512 sheet: -3.35 (0.33), residues: 108 loop : -2.58 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 692 HIS 0.008 0.001 HIS A 430 PHE 0.014 0.001 PHE A 316 TYR 0.022 0.002 TYR B 390 ARG 0.002 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 798) hydrogen bonds : angle 4.12084 ( 2322) covalent geometry : bond 0.00360 (21964) covalent geometry : angle 0.62907 (29484) *********************** 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 315 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: A 531 VAL cc_start: 0.8732 (t) cc_final: 0.8402 (m) REVERT: A 544 TYR cc_start: 0.6399 (m-80) cc_final: 0.6146 (m-80) REVERT: A 650 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.5106 (m-80) REVERT: B 211 GLU cc_start: 0.7825 (pm20) cc_final: 0.7541 (pm20) REVERT: B 544 TYR cc_start: 0.6412 (m-80) cc_final: 0.6170 (m-80) REVERT: B 581 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6846 (mptt) REVERT: B 650 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.5121 (m-80) REVERT: B 726 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7761 (mm-30) REVERT: C 211 GLU cc_start: 0.7825 (pm20) cc_final: 0.7415 (pm20) REVERT: C 254 TYR cc_start: 0.7955 (m-80) cc_final: 0.7714 (m-10) REVERT: C 531 VAL cc_start: 0.8669 (t) cc_final: 0.8364 (m) REVERT: C 540 TYR cc_start: 0.8403 (t80) cc_final: 0.7842 (t80) REVERT: C 544 TYR cc_start: 0.6327 (m-80) cc_final: 0.6105 (m-80) REVERT: C 581 LYS cc_start: 0.6940 (mmtt) cc_final: 0.6723 (mptt) REVERT: D 254 TYR cc_start: 0.7968 (m-80) cc_final: 0.7748 (m-80) REVERT: D 544 TYR cc_start: 0.6280 (m-80) cc_final: 0.5982 (m-80) REVERT: D 650 TYR cc_start: 0.5480 (OUTLIER) cc_final: 0.4878 (m-80) outliers start: 44 outliers final: 25 residues processed: 305 average time/residue: 0.3258 time to fit residues: 156.8664 Evaluate side-chains 264 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 591 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 499 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 154 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 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 116 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 227 GLN A 430 HIS B 227 GLN C 227 GLN D 227 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 = 0.3861 r_free = 0.3861 target = 0.146018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110571 restraints weight = 33264.677| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.26 r_work: 0.3141 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21964 Z= 0.202 Angle : 0.658 8.005 29484 Z= 0.332 Chirality : 0.043 0.181 3232 Planarity : 0.004 0.050 3556 Dihedral : 19.459 112.490 3812 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.47 % Favored : 93.20 % Rotamer: Outliers : 2.68 % Allowed : 9.39 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2456 helix: -1.19 (0.12), residues: 1540 sheet: -2.82 (0.37), residues: 108 loop : -2.54 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 692 HIS 0.008 0.001 HIS D 301 PHE 0.015 0.002 PHE B 316 TYR 0.018 0.002 TYR B 451 ARG 0.006 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 798) hydrogen bonds : angle 4.18874 ( 2322) covalent geometry : bond 0.00490 (21964) covalent geometry : angle 0.65792 (29484) *********************** 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 304 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 2.139 Fit side-chains REVERT: A 544 TYR cc_start: 0.6455 (m-80) cc_final: 0.6232 (m-80) REVERT: A 650 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.4535 (m-80) REVERT: A 725 ASP cc_start: 0.8085 (t0) cc_final: 0.7791 (t0) REVERT: B 211 GLU cc_start: 0.8164 (pm20) cc_final: 0.7752 (pm20) REVERT: B 581 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6884 (mptt) REVERT: B 650 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.4559 (m-80) REVERT: B 679 GLU cc_start: 0.7253 (mp0) cc_final: 0.7048 (mp0) REVERT: B 726 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 211 GLU cc_start: 0.8099 (pm20) cc_final: 0.7677 (pm20) REVERT: C 254 TYR cc_start: 0.8116 (m-80) cc_final: 0.7902 (m-80) REVERT: C 581 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6793 (mptt) REVERT: C 603 VAL cc_start: 0.7622 (t) cc_final: 0.7284 (p) REVERT: C 650 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: D 544 TYR cc_start: 0.6356 (m-80) cc_final: 0.6060 (m-80) REVERT: D 603 VAL cc_start: 0.7633 (t) cc_final: 0.7325 (p) REVERT: D 650 TYR cc_start: 0.5451 (OUTLIER) cc_final: 0.4689 (m-80) outliers start: 59 outliers final: 40 residues processed: 292 average time/residue: 0.3129 time to fit residues: 145.6672 Evaluate side-chains 275 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 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 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 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 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 685 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 430 HIS B 255 GLN C 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108504 restraints weight = 32866.494| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.38 r_work: 0.3111 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21964 Z= 0.183 Angle : 0.633 8.015 29484 Z= 0.321 Chirality : 0.042 0.182 3232 Planarity : 0.004 0.050 3556 Dihedral : 19.164 111.130 3812 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.07 % Favored : 93.61 % Rotamer: Outliers : 2.63 % Allowed : 11.03 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2456 helix: -0.97 (0.13), residues: 1576 sheet: -2.53 (0.39), residues: 116 loop : -2.41 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 559 HIS 0.007 0.001 HIS A 430 PHE 0.015 0.001 PHE D 316 TYR 0.016 0.002 TYR A 451 ARG 0.004 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 798) hydrogen bonds : angle 4.06762 ( 2322) covalent geometry : bond 0.00441 (21964) covalent geometry : angle 0.63326 (29484) *********************** 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 289 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 231 time to evaluate : 2.069 Fit side-chains REVERT: A 529 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: A 650 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.4414 (m-80) REVERT: B 211 GLU cc_start: 0.7823 (pm20) cc_final: 0.7460 (pm20) REVERT: B 544 TYR cc_start: 0.6231 (m-80) cc_final: 0.5968 (m-80) REVERT: B 581 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6923 (mptt) REVERT: B 650 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.4445 (m-80) REVERT: B 726 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 211 GLU cc_start: 0.7810 (pm20) cc_final: 0.7439 (pm20) REVERT: C 529 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: C 544 TYR cc_start: 0.6211 (m-80) cc_final: 0.5935 (m-80) REVERT: C 581 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6898 (mptt) REVERT: C 603 VAL cc_start: 0.7586 (t) cc_final: 0.7229 (p) REVERT: C 650 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.4657 (m-80) REVERT: D 122 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8467 (ttp80) REVERT: D 650 TYR cc_start: 0.5328 (OUTLIER) cc_final: 0.4651 (m-80) outliers start: 58 outliers final: 42 residues processed: 276 average time/residue: 0.3191 time to fit residues: 140.0010 Evaluate side-chains 272 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 2.486 ------------------------------------------------------------------------------- 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 529 GLN 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 591 LEU Chi-restraints excluded: chain A residue 605 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 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 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 529 GLN 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 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 Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 118 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112018 restraints weight = 32903.159| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.17 r_work: 0.3195 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21964 Z= 0.122 Angle : 0.574 8.101 29484 Z= 0.290 Chirality : 0.040 0.176 3232 Planarity : 0.003 0.044 3556 Dihedral : 18.536 104.596 3812 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.38 % Rotamer: Outliers : 2.09 % Allowed : 11.93 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2456 helix: -0.61 (0.13), residues: 1568 sheet: -2.09 (0.42), residues: 116 loop : -2.39 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.007 0.001 HIS A 430 PHE 0.013 0.001 PHE D 316 TYR 0.013 0.001 TYR C 460 ARG 0.005 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 798) hydrogen bonds : angle 3.87866 ( 2322) covalent geometry : bond 0.00283 (21964) covalent geometry : angle 0.57368 (29484) *********************** 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 273 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 2.320 Fit side-chains REVERT: A 122 ARG cc_start: 0.8777 (ttm170) cc_final: 0.8499 (ttp80) REVERT: A 529 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: A 544 TYR cc_start: 0.6324 (m-80) cc_final: 0.6080 (m-80) REVERT: A 650 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.4063 (m-80) REVERT: B 122 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8468 (ttp80) REVERT: B 211 GLU cc_start: 0.8008 (pm20) cc_final: 0.7634 (pm20) REVERT: B 544 TYR cc_start: 0.6207 (m-80) cc_final: 0.5956 (m-80) REVERT: B 581 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6791 (mptt) REVERT: B 650 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.4243 (m-80) REVERT: B 726 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8006 (mm-30) REVERT: C 122 ARG cc_start: 0.8788 (mtm180) cc_final: 0.8488 (ttp80) REVERT: C 159 MET cc_start: 0.7927 (mmm) cc_final: 0.7588 (mmm) REVERT: C 211 GLU cc_start: 0.8009 (pm20) cc_final: 0.7636 (pm20) REVERT: C 529 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: C 544 TYR cc_start: 0.6202 (m-80) cc_final: 0.5938 (m-80) REVERT: C 581 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6746 (mptt) REVERT: C 650 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4328 (m-80) REVERT: D 122 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8550 (ttp80) REVERT: D 544 TYR cc_start: 0.6186 (m-80) cc_final: 0.5849 (m-80) REVERT: D 650 TYR cc_start: 0.5159 (OUTLIER) cc_final: 0.4501 (m-80) outliers start: 46 outliers final: 33 residues processed: 263 average time/residue: 0.2998 time to fit residues: 126.2452 Evaluate side-chains 244 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 529 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 591 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 A residue 732 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 MET 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 732 LEU 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 529 GLN 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 C residue 732 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 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 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3896 r_free = 0.3896 target = 0.149063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112563 restraints weight = 32784.366| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.14 r_work: 0.3210 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3768 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= 0.114 Angle : 0.562 8.637 29484 Z= 0.284 Chirality : 0.039 0.176 3232 Planarity : 0.003 0.040 3556 Dihedral : 18.012 103.078 3812 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 1.91 % Allowed : 12.34 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2456 helix: -0.31 (0.13), residues: 1576 sheet: -1.63 (0.44), residues: 116 loop : -2.40 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.006 0.001 HIS A 430 PHE 0.014 0.001 PHE A 316 TYR 0.020 0.001 TYR B 460 ARG 0.005 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 798) hydrogen bonds : angle 3.79138 ( 2322) covalent geometry : bond 0.00261 (21964) covalent geometry : angle 0.56197 (29484) *********************** 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 265 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 2.490 Fit side-chains REVERT: A 122 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8533 (ttp80) REVERT: A 529 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: A 544 TYR cc_start: 0.6257 (m-80) cc_final: 0.6039 (m-80) REVERT: A 650 TYR cc_start: 0.4753 (OUTLIER) cc_final: 0.3845 (m-80) REVERT: B 122 ARG cc_start: 0.8781 (ttm170) cc_final: 0.8479 (ttp80) REVERT: B 211 GLU cc_start: 0.7991 (pm20) cc_final: 0.7637 (pm20) REVERT: B 544 TYR cc_start: 0.6108 (m-80) cc_final: 0.5877 (m-80) REVERT: B 581 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6747 (mptt) REVERT: B 650 TYR cc_start: 0.4906 (OUTLIER) cc_final: 0.4043 (m-80) REVERT: B 726 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 122 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8527 (ttp80) REVERT: C 159 MET cc_start: 0.7959 (mmm) cc_final: 0.7631 (mmm) REVERT: C 211 GLU cc_start: 0.8003 (pm20) cc_final: 0.7654 (pm20) REVERT: C 529 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: C 544 TYR cc_start: 0.6188 (m-80) cc_final: 0.5941 (m-80) REVERT: C 581 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6811 (mptt) REVERT: C 650 TYR cc_start: 0.4979 (OUTLIER) cc_final: 0.4181 (m-80) REVERT: D 122 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8578 (ttp80) REVERT: D 570 GLN cc_start: 0.8171 (tt0) cc_final: 0.7970 (tt0) REVERT: D 650 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4330 (m-80) outliers start: 42 outliers final: 33 residues processed: 258 average time/residue: 0.3092 time to fit residues: 126.6155 Evaluate side-chains 244 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 584 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 A residue 732 LEU 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 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 732 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 529 GLN 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 732 LEU 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 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 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 200 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 81 optimal weight: 0.1980 chunk 222 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.0370 chunk 172 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.152292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115303 restraints weight = 32816.488| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.22 r_work: 0.3235 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21964 Z= 0.092 Angle : 0.534 8.122 29484 Z= 0.271 Chirality : 0.038 0.168 3232 Planarity : 0.003 0.041 3556 Dihedral : 17.262 98.542 3812 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.77 % Allowed : 12.43 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2456 helix: 0.10 (0.13), residues: 1568 sheet: -1.48 (0.46), residues: 112 loop : -2.28 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 739 HIS 0.006 0.001 HIS A 430 PHE 0.012 0.001 PHE D 310 TYR 0.014 0.001 TYR D 460 ARG 0.004 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 798) hydrogen bonds : angle 3.65265 ( 2322) covalent geometry : bond 0.00198 (21964) covalent geometry : angle 0.53363 (29484) *********************** 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 275 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 2.154 Fit side-chains REVERT: A 122 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8565 (ttp80) REVERT: A 529 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: A 544 TYR cc_start: 0.6112 (m-80) cc_final: 0.5864 (m-80) REVERT: A 650 TYR cc_start: 0.4434 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: B 122 ARG cc_start: 0.8787 (ttm170) cc_final: 0.8527 (ttp80) REVERT: B 211 GLU cc_start: 0.8051 (pm20) cc_final: 0.7715 (pm20) REVERT: B 544 TYR cc_start: 0.5945 (m-80) cc_final: 0.5734 (m-80) REVERT: B 581 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6690 (mptt) REVERT: B 650 TYR cc_start: 0.4615 (OUTLIER) cc_final: 0.3691 (m-80) REVERT: B 726 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 122 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8573 (ttp80) REVERT: C 159 MET cc_start: 0.7954 (mmm) cc_final: 0.7651 (mmm) REVERT: C 211 GLU cc_start: 0.8036 (pm20) cc_final: 0.7686 (pm20) REVERT: C 529 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6591 (tt0) REVERT: C 544 TYR cc_start: 0.6034 (m-80) cc_final: 0.5824 (m-80) REVERT: C 650 TYR cc_start: 0.4781 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: D 650 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.4276 (m-80) outliers start: 39 outliers final: 22 residues processed: 267 average time/residue: 0.3156 time to fit residues: 132.4096 Evaluate side-chains 243 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 541 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 485 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 MET 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 217 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.151223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115043 restraints weight = 32576.421| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.18 r_work: 0.3222 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21964 Z= 0.101 Angle : 0.553 8.713 29484 Z= 0.280 Chirality : 0.038 0.174 3232 Planarity : 0.003 0.041 3556 Dihedral : 17.035 95.725 3812 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.32 % Allowed : 13.20 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2456 helix: 0.17 (0.13), residues: 1596 sheet: -1.05 (0.47), residues: 108 loop : -2.43 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 559 HIS 0.007 0.001 HIS B 430 PHE 0.014 0.001 PHE C 316 TYR 0.016 0.001 TYR B 460 ARG 0.004 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 798) hydrogen bonds : angle 3.70630 ( 2322) covalent geometry : bond 0.00229 (21964) covalent geometry : angle 0.55270 (29484) *********************** 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: 29 poor density : 230 time to evaluate : 2.203 Fit side-chains REVERT: A 122 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8589 (ttp80) REVERT: A 278 VAL cc_start: 0.9052 (t) cc_final: 0.8836 (t) REVERT: A 529 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: A 650 TYR cc_start: 0.4521 (OUTLIER) cc_final: 0.3635 (m-80) REVERT: B 122 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8544 (ttp80) REVERT: B 211 GLU cc_start: 0.8055 (pm20) cc_final: 0.7715 (pm20) REVERT: B 544 TYR cc_start: 0.5993 (m-80) cc_final: 0.5716 (m-80) REVERT: B 581 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6658 (mptt) REVERT: B 650 TYR cc_start: 0.4611 (OUTLIER) cc_final: 0.3679 (m-80) REVERT: B 726 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8014 (mm-30) REVERT: C 122 ARG cc_start: 0.8820 (mtm180) cc_final: 0.8584 (ttp80) REVERT: C 159 MET cc_start: 0.7962 (mmm) cc_final: 0.7641 (mmm) REVERT: C 211 GLU cc_start: 0.8039 (pm20) cc_final: 0.7687 (pm20) REVERT: C 529 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: C 650 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.3787 (m-80) REVERT: D 122 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8663 (ttp80) REVERT: D 278 VAL cc_start: 0.9035 (t) cc_final: 0.8814 (t) REVERT: D 650 TYR cc_start: 0.4708 (OUTLIER) cc_final: 0.4136 (m-80) outliers start: 29 outliers final: 18 residues processed: 254 average time/residue: 0.3123 time to fit residues: 125.8504 Evaluate side-chains 242 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR 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 541 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 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 MET 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 151 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 237 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111563 restraints weight = 32899.960| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.29 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21964 Z= 0.132 Angle : 0.591 8.705 29484 Z= 0.298 Chirality : 0.040 0.182 3232 Planarity : 0.003 0.040 3556 Dihedral : 17.143 96.333 3812 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 1.41 % Allowed : 13.57 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2456 helix: 0.27 (0.13), residues: 1532 sheet: -1.01 (0.47), residues: 108 loop : -2.35 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.007 0.001 HIS C 430 PHE 0.015 0.001 PHE C 316 TYR 0.016 0.001 TYR C 460 ARG 0.004 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 798) hydrogen bonds : angle 3.84114 ( 2322) covalent geometry : bond 0.00314 (21964) covalent geometry : angle 0.59067 (29484) ********************** 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 257 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 2.077 Fit side-chains REVERT: A 122 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8541 (ttp80) REVERT: A 278 VAL cc_start: 0.8952 (t) cc_final: 0.8735 (t) REVERT: A 529 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: A 650 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.3713 (m-80) REVERT: B 122 ARG cc_start: 0.8795 (ttm170) cc_final: 0.8534 (ttp80) REVERT: B 211 GLU cc_start: 0.7792 (pm20) cc_final: 0.7489 (pm20) REVERT: B 544 TYR cc_start: 0.6103 (m-80) cc_final: 0.5872 (m-80) REVERT: B 581 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6832 (mptt) REVERT: B 650 TYR cc_start: 0.4737 (OUTLIER) cc_final: 0.3909 (m-80) REVERT: B 726 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 122 ARG cc_start: 0.8799 (mtm180) cc_final: 0.8540 (ttp80) REVERT: C 159 MET cc_start: 0.7945 (mmm) cc_final: 0.7525 (mmm) REVERT: C 211 GLU cc_start: 0.7802 (pm20) cc_final: 0.7487 (pm20) REVERT: C 529 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6595 (tt0) REVERT: C 677 MET cc_start: 0.6748 (mtm) cc_final: 0.6521 (mtm) REVERT: D 278 VAL cc_start: 0.9001 (t) cc_final: 0.8799 (t) REVERT: D 650 TYR cc_start: 0.4636 (OUTLIER) cc_final: 0.4084 (m-80) outliers start: 31 outliers final: 21 residues processed: 251 average time/residue: 0.3203 time to fit residues: 128.1188 Evaluate side-chains 249 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 605 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 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 541 LEU 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 323 MET 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 190 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111340 restraints weight = 32622.058| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.28 r_work: 0.3167 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21964 Z= 0.134 Angle : 0.593 8.750 29484 Z= 0.299 Chirality : 0.040 0.187 3232 Planarity : 0.003 0.040 3556 Dihedral : 17.137 96.259 3812 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 1.32 % Allowed : 13.66 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2456 helix: 0.22 (0.13), residues: 1532 sheet: -0.96 (0.47), residues: 108 loop : -2.32 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.007 0.001 HIS C 430 PHE 0.015 0.001 PHE A 316 TYR 0.016 0.001 TYR C 460 ARG 0.004 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 798) hydrogen bonds : angle 3.87081 ( 2322) covalent geometry : bond 0.00317 (21964) covalent geometry : angle 0.59281 (29484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12600.12 seconds wall clock time: 218 minutes 17.59 seconds (13097.59 seconds total)